10 (Almost) Secret Tokyo Hidden Gems You’ve Never Heard Of

When it comes to cities as busy and famous as Tokyo, it’s almost inevitable that you’ll run into other tourists at popular attractions. In saying that, with a little research up your sleeve it’s possible to blend in with locals and unearth some intriguing Tokyo hidden gems. You’re about to learn there are many dotted throughout the city, a number of which foreign tourists don’t yet know about!

To bring you this travel guide to secret spots in Tokyo, I’ve teamed up with the amazing and lovely Alex from Pretty Pastel Please over on YouTube. Her video on exclusively eating 7-11 food in Japan for a week has been insanely popular and proves eating out in this amazing country doesn’t have to be as expensive as you think!

I particularly love Alex’s vlog, One Week in Japan Wearing Only Japanese Thrift Store Clothes, which demonstrates the ways she loves being a fellow “invisible tourist” in Japan. In part, this means we follow her journey immersing herself in local culture, getting out of the well-trodden areas, having a go at the language and seeking out the undiscovered hidden gems.

As Japan lovers and content creators, Alex and I have both spent much time exploring the popular and lesser-known attractions in Tokyo and hope to inspire you, too. By sharing our joint experiences with you at these secret places in Tokyo in written and video format, we’re certain our findings will help you enrich your visit in a unique way.

If you’re ready to learn about 10 fascinating “only in Tokyo” experiences to transform your visit from ordinary to extraordinary, read on for more!

Here’s 10 (almost) secret hidden gems in Tokyo to add to your itinerary

As 10 attractions scattered throughout Tokyo would be a lot to cram into a single day, the below travel guide can be followed over two days. I’ve done the hard yards for you and figured out the most efficient way to visit them geographically and according to public transport options nearby. It’s simple to follow along throughout the day!

Alternatively, these destinations can be cherry-picked and woven into your own Tokyo itinerary depending on your interests. They’re also part of my detailed Japan 3 week itinerary if you’ll be visiting for a little while. You may also like my guide to Kyoto hidden gems so take a look once you’re done here.

To visit these places I highly recommend using Google Maps on your smartphone to guide you most of the way, it’s super helpful for getting around Japan. In order to avoid unnecessary data charges from your mobile provider, many travellers to Japan (including myself) prefer to hire a pocket wifi device or 4G SIM card for their phone. Click through to book your own portable wifi or 4G SIM card in advance here.

Get ready to explore Tokyo off the beaten path and discover some traditional Japanese treasures, indulge in photo-worthy sweet treats and enjoy fascinating sights that many tourists don’t have the chance to uncover during their first trip to Tokyo.

How many have you heard of? 

1. Start the day at Gotoku-ji Temple, Setagaya

Do you love maneki neko? You’re in luck as there is a temple entirely dedicated to them in the Setagaya neighbourhood of Tokyo! They’re one of the many famous things in Japan. In case you aren’t familiar with the term, maneki neko refers to the waving or “beckoning” cat trinkets you’ve likely seen in your favourite Asian restaurant or grocery store at home. But why are they so widespread?

There’s a reason why these cute little felines are so popular. Legend says during heavy rain, a feudal lord was sitting beneath a tree when a cat appeared nearby. It raised its paw, beckoning the man over from his shelter. As the man made his way towards the cat, lightning struck the tree and it came crashing down exactly where he had sat. This is why the cats are known as “beckoning” or “fortune” cats.

It’s believed that Gotokuji temple is the origin of these lucky charms. As you make your way through the temple’s entrance past the burning incense, you’ll notice countless fortune cats clustered together, left by visitors to the temple. The maneki neko come in a range of sizes and all raise their right paw at this temple, meaning they are beckoning good fortune and success towards you!

TIP: The GPS on Google Maps took me to the back of the temple where there was no visible entry. Follow the signage and walk 400m around the block to the front entrance gate.

Visiting Gotoku-ji Temple

• Cost: Free entry, small 3cm cats 500 JPY, to large 30cm cats 5,000 JPY
• Nearest station: Miyanosaka Station (Tokyu Setagaya Line), 5 min walk, or Gotokuji Station (Odakyu Line), 10 min walk.
• Opening hours: 8:30am – 5:00pm daily
• More info: Atlas Obscura 
• Featured in Pretty Pastel Please video at 01:24

2. Enjoy morning tea at Shiro-Hige Cream Puff Factory, Setagaya

Here’s one for the Ghibli fans. In the trendy neighbourhood of Setagaya you’re able to adopt your very own miniature Totoro, in delectable cream-puff form! The store is actually run by the sister in law of Miyazaki Hayao, the co-founder of the popular Studio Ghibli animation studio. 

Shiro-Hige Cream Puff Factory is the only place in the entire world with permission to create Totoro-shaped treats, so not only is this a very unique Tokyo experience, it’s the only of its kind globally. 

There’s a reason why we’re visiting this earlier in the day. As the cream puffs are only made in the mornings, I’d suggest getting here before opening to secure your own little Totoro before they sell out. Other Ghibli souvenirs are available, too.

The Totoro cream puffs come in a variety of flavours, some of which are limited and seasonal. But chocolate and original custard fillings are available year-round. It’s easy to tell what filling the cream puff has by checking the little ornament on Totoro’s head and matching it to this chart. You can opt to eat-in upstairs (if you sit and purchase a drink) or bring Totoro with you as take-out for later.

As I walked in, the aroma of these freshly baked sweets was incredible! I wish they could bottle up the sweet smell or turn it into a candle – it’s SO good!

TIP: This is mainly a quiet residential area so please do your best to “be invisible” on your way to the café and keep noise to a minimum for locals.

Visiting Shiro-Hige Cream Puff Factory

• Cost: 420 – 460 JPY per cream puff
• Nearest station: Setagaya-Daita (Odakyu Odawara line), 3 mins walk.
• Opening hours: 10:30am – 7:00pm
• More info: SoraNews24 
• Featured in Pretty Pastel Please video at 05:27

3. Indulge in an early lunch in Yanaka Ginza

Unfortunately, our next one featured in the video closed permanently in April 2023. The best way to describe Café Ron Ron in Harajuku was a high tea on rotation, much like a sushi train but of quality desserts.

As a replacement for Café Ron Ron for lunch, I recommend a neighbourhood often overlooked by tourists in Tokyo: Yanaka. Featuring preserved old world-charm and Showa-era nostalgia, Yanaka survived the firebombing of Tokyo during WWII unlike much of the city.

The Yanaka Ginza shopping area is lined with small cafes, eateries and boutiques selling handmade crafts and foods by local artisans. This Yanaka local foodie tour will help you make the most of your time in this off the beaten path Tokyo neighbourhood.

You’ll find traditionally-made sweets, snacks, clothing, Japanese beverages such as yuzu and sake, and even treats exclusive to this neighbourhood. Keep your eyes out for lucky cat statues dotted around!

Visiting Yanaka Ginza

• Nearest station: JR Nippori Station
• Opening hours:Will vary by store, but generally the hours range from 9:30am – midnight (non-food establishments close earlier).
• More info: How to eat your way through Yanaka Ginza 

TIP: Read my Shibuya Sky tips to learn from mistakes I made during my first visit, and how you can plan your perfect experience! You can also buy Shibuya Sky tickets in advance here.

Visiting Shibuya Sky

• Cost: Adults JPY 2000 (discounted if bought online in advance, plus 100 JPY for locker to store all your belongings. Only your camera/smartphone is permitted on the rooftop).
• Nearest station: JR Shibuya Station, 4 min walk. Take the lift to Level 14, then the express lift to Shibuya Sky will take you the rest of the way.
• Opening hours: 9:00am – 11:00pm
• More info: Shibuya Scramble Square
• Featured in Pretty Pastel Please video at 12:42

5. Finish the day exploring one of the Tokyo hidden neighbourhoods: Jiyugaoka, Meguro 

If you fancy a little slice of Europe during your time in Tokyo, be sure to head to stylish Jiyugaoka in the Meguro neighbourhood. This is one of the best hidden places in Tokyo because it’s home to a bunch of narrow alleyways lined with trendy boutiques, unique European-style cafés and specialty stores. It’s possible to stroll down a Parisian-themed street one moment then an Italian one the next!

While a picturesque arched bridge and gondola will have you feeling like you’ve stepped into a miniature Venice, a drawcard to Jiyugaoka is a complex of eight sweet stores called Sweets Forest. Stop here for delicious breakfast crepes to satisfy both sweet and savoury tastes, mouthwatering cakes that look too good to eat and of course, a huge selection of sweets. The baked goods from the Bake Cheese Tart store are also popular with locals.

As usual in Japan, you never have to venture too far to find tradition. If you prefer to enjoy some matcha tea and wagashi sweets overlooking a beautiful Japanese garden, Kosoan teahouse is your best bet.

TIP: The La Vita area is where you can find the Venice-style bridge. This is located within a complex of small businesses. Pop in to a few and purchase some souvenirs or enjoy a massage. Please remember to “be invisible” here as to not disrupt locals whilst you explore.

Visiting Jiyugaoka

• Cost: Free to explore
• Nearest station: Jiyugaoka Subway Station (Tokyu Line), 5 min walk.
• Opening hours: Many stores open at either 10:00am or 11:00am and close at 8:00pm.
• More info: GoTokyo
• Featured in Pretty Pastel Please video at 14:42

6. Begin your second day at Asakusa-jinja, Asakusa 

While you’re in Asakusa there’s no doubt you’d plan to visit Senjo-ji, Tokyo’s most beloved and oldest Buddhist temple. But did you know one of Tokyo’s oldest and original shrines is quietly tucked away next door? Asakusa Shrine, or Asakusa-jinja honours the men who founded Senso-ji and is marked by a large stone torii gate at its entrance.

What’s special about this Tokyo hidden gem is that unlike the more famous attraction next door, Asakusa-jinja survived the firebombing of the city during WWII. In actual fact, it is one of only two structures in this area to have endured the test of time since the 17th century. 

Although the site of Senso-ji dates back to the 7th century, its collection of buildings are reconstructed. If you look closely behind the Hozomon gate of Senso-ji today some trees still bear deep scars of the atrocity, which puts the remarkable survival of adjoining Asakusa-jinja into perspective. 

An unusual feature of Asakusa-jinja is two stone statues depicting lion-dogs beneath a parasol. These married stone animals are said to be quite precious as they date back to the Edo period (1603 – 1868) and are thought to bring success and happy marriages. Despite being married for centuries, they still look pretty happy!

Due to this historical significance Asakusa-jinja is an Important Cultural Property of Japan. It truly is a special gift from the past.

Visiting Asakusa-jinja

• Cost: Free entry
• Nearest station: Asakusa Metro Station (Toei Asakusa Line), 4 mins walk.
• Opening hours:  9:00am – 4:30pm
• More info: Asakusa Station 
• Featured in Pretty Pastel Please video at 17:07

7. Hop on over to Nezu Shrine, Ueno

If you love the idea of Kyoto’s famous vermilion torii gates at Fushimi Inari Taisha but without the crowds, Nezu Shrine in Ueno is for you! This is a great alternative to one of Japan’s most famous attractions and the best part is it’s practically undiscovered by foreign tourists. You could have the entire place to yourself during your visit, which is a rare treat. 

Also known as Nedu-jinja, Nezu Shrine is actually one of the oldest shrines in the country, dating back over 1,000 years. Surrounded by dense trees and gardens, the grounds also feature a lovely wooden viewing platform overlooking a koi pond. Modelled after the stunning Toshogu Shrine in Nikko, the intricate wooden Shinto structures making up this temple are considered Important Cultural Properties of Japan.

Nezu Shrine is an underrated Tokyo hidden gem and is mostly known for its vibrant azalea flower festival during the spring. A secondary shrine, Otome Inari-jinja can also be visited on the premises and its peaceful setting is a lovely place to soak up some tranquility in busy Tokyo.

The exquisite attention to detail on the shrine building had me captivated for ages, its visual link to Toshogu Shrine is beautifully obvious. Nezu Shrine quickly became one of my favourite Tokyo hidden gems, for sure!

Visiting Nezu Shrine

• Cost: Free entry
• Nearest station: Nezu Metro Station (Chiyoda Line), 3 mins walk.
• Opening hours: Reception 9:00am – 4:30pm
• More info: Japan Visitor 
• Featured in Pretty Pastel Please video at 18:37

8. Enjoy a sweet refreshment at 2D Café Shin-Okubo, Shinjuku

Have you ever wondered what it would be like to jump inside the pages of your favourite comic book? The 2D Café in Shinjuku is the closest thing to making that fantasy a reality! The idea for this café actually originated in South Korea and has made its way to Japan’s capital.

On entering the café, you’ll notice everyday furniture and other items appear to have been carefully hand-drawn in black marker against a white backdrop. This clever technique applied to tables, chairs and walls creates the illusion of a real-life illustration here in the Shin-Okubo area of Shinjuku, also known as Korea Town. 

In saying that, the monochrome drawing truly comes to life when you order a fruity bubble tea or Korean-style shaved ice with fruit and whipped cream. The bright colours highly contrast against their seemingly flat monochrome surroundings, which makes for great photo opportunities! Grabbing a refreshment here is definitely one of the alternative things to do in Tokyo.

My pineapple shaved ice drink tasted like a tropical holiday in my mouth! Really delicious.

TIP: If using your phone’s GPS and Google Maps to find 2D Café, it may take you to the rear entrance the second street parallel to the train tracks. There was a sign on the door entirely in Japanese I couldn’t read, so I went around to the front entrance, which is the street directly opposite the train tracks. Saves you walking awkwardly through the tables to get to the front counter!

Visiting 2D Café

• Cost: Menu items range from 600 – 1500 JPY
• Nearest station: JR Shin-Okubo Station (Yamanote Line), 3 min walk.
• Opening hours: 11:00am – 11:00pm daily
• More info: Japan Today 
• Featured in Pretty Pastel Please video at 23:12

9. Enjoy matcha tea at Hamarikyu Gardens & Nakajima no Ochaya Teahouse, Minato 

One of Tokyo’s most underrated gems is Hamarikyu Gardens. An interesting feature that differentiates the ponds and canals of this landscaped garden from others is they’re composed of seawater. Being connected to Tokyo Bay means the waters rise and fall with the tides. 

During the Edo period the park was a duck hunting ground for feudal lords, even a memorial remains that is dedicated to the victim ducks’ souls. Formerly a detached palace to the Imperial Family, the gardens were gifted to the public in 1945 after WWII.

Keep a lookout for the 300-year old pine tree still thriving today, although some of its limbs are so lengthy they’re held up by wooden supports. Imagine the stories this tree could tell if it were able to speak, it’s been a silent witness to many events throughout the centuries! Other pine trees have been so meticulously pruned with care over the decades, they look like giant bonsai.

A pleasant way to relax in Hamarikyu Gardens is to pay a visit to Nakajima no Ochaya teahouse. This traditional thatched-roof teahouse is floating on an island boardwalk, overlooking the main pond and surrounding gardens. It’s so lovely to enjoy a bowl of hot or cold matcha tea on the tatami mats as the water laps beneath your feet. 

Visiting Hamarikyu Gardens

• Cost: Gardens entry fee 300 JPY, tea + wagashi 510 JPY
• Nearest station: Shibakoen Subway Station (Mita Line), 6mins walk or 25mins walk from Zojo-ji Temple (further down the page).
• Opening hours: 9:00am – 5:00pm
• More info: TokyoPark.org
• Featured in Pretty Pastel Please video at 24:17

10. Finish your day at Zojo-ji Temple, Minato

If you love learning more about Japanese culture and how it is beautifully intertwined in everyday life, a visit to Zojo-ji Temple is a memorable experience. Old meets new so seamlessly here, with the modern Tokyo Tower piercing the sky behind Zojo-ji’s traditional main hall building. 

Zojo-ji is a significant Tokyo attraction as it has ties to the Tokugawa rulers of Japan during the Edo period. Although this structure was severely damaged during the firebombing of Tokyo in WWII, the origins Zojo-ji date back to the 14th century. The temple’s huge main gate is one of the oldest in Tokyo, having been standing here since 1622.

The most moving part of visiting Zoji-ji is undoubtedly seeing the hundreds (if not thousands) of Jizo carefully placed throughout the temple grounds. These colourfully-decorated stone statues are dedicated to the safety and growth of children, as well as acting as a memorial to miscarried and stillborn babies. The knitted red hats and aprons are said to keep them warm and protected. I even found myself choking up at the thought of this idea!

TIP: Please, don’t be an annoying tourist here and make sure you act in a quiet and respectful way during your visit. Take a moment to understand the significance of these little statues and remember to respect the rules of not touching them as the signage requests.

Visiting Zojo-ji Temple

• Cost: Free entry
• Nearest station: Shibakoen Subway Station (Mita Line), 7mins walk.
• Opening hours: 9:00am – 5:00pm
• More info: Zojo-ji Official Website
• Featured in Pretty Pastel Please video at 28:52

Concluding visiting Tokyo off the beaten path

That’s a wrap for these inspiring best hidden gems in Tokyo! From stunning shrines, quirky cafés, tranquil gardens to newer Tokyo attractions that haven’t quite made it big with foreigners yet, I hope this guide managed to surprise and inspire you.

Now you know exactly where to find them and what to expect, how many of these hidden places in Tokyo will you add to your Japan itinerary? Let me know in the comments below!

If you’re after more inspiration, I have many more travel guides and itineraries here on my Japan travel blog. From finding hidden gems, detailed city guides, best time to visit for cherry blossoms and more, I have your Japan trip covered.

As this guide to Tokyo forms part of my series on Japan’s Golden Route, if you’re interested take a look at my separate guides for Japan’s off the beaten path destinations, more hidden gems and reviews of cultural experiences to enrich your trip.

Want to learn my strategies for how to “blend in” anywhere around the globe? Find out by reading my #1 Amazon New Release Book!