I've made posts about Hakone, Okinawa, and various other places, but how have I not made one on Tokyo?! Also, this post will be so handy for me as, somewhere along the way, I've apparently become a freelance travel agent as most of the DM's I get are all questions about the best "secret spots" in Tokyo.
Unfortunately for them, the secret spots in my daily itinerary are usually my school, my local gym, the arcade down the road, and the grocery store. Obviously my routine is lacking in flashing lights and visits from Godzilla... but I have found a few greats spots during the three years that I've been living here. I'll try to provide an eclectic mix of popular and unknown places that might appeal to a variety of travelers. I'll also give you a short pros and cons list for each location just so you have an idea of what you might be getting yourself into. Enjoy!

Ikegami Honmonji - A Buddhist Temple in the Ota Ward

Honmonji's famous five-story pagoda.

That beloved, vermilion color. 

Pros:

• ⧫ It's free and it's always open!
• ⧫ You can catch a very lively festival there in mid-October.
• ⧫ It's a gorgeous place to view cherry blossoms in the spring.
• ⧫ Apart from festival season, it's never crowded.
• ⧫ There are many buildings and structures to see.
• ⧫ You can easily find lots of information on each structure in English.

Cons:

• ⧫ It's a bit far for people who are staying in the northern areas of Tokyo (approx. 40-50 minutes from Shinjuku).
• ⧫ There are a lot of stairs (96 stone stairs to the gate) and slopes so be prepared to walk a fair amount. 
• ⧫ It's in the middle of a very residential area so there's nothing you could easily jump to after. 

Mori Building Digital Art Museum - A Hands-On Art Exhibit in Odaiba

This is the most well-known room at the exhibit in Odaiba

Lots of rooms for the little ones to enjoy too!

Pros:

• ⧫ There are only a select number of tickets sold for each day, so it's not wall-to-wall with people. 
• ⧫ The museum is quite large so everyone can move around easily and at their own pace.
• ⧫ It's definitely a unique experience that you can't get elsewhere.
• ⧫ There are no maps and so you can find something new every time you go. 
• ⧫ There are a lot of other interesting things to see and do right beside this museum. 

Cons:

• ⧫ Be sure to meet your friends outside of the venue! You will never find them if you try to meet up inside of the museum.
• ⧫ Don't wear a skirt. There are lots of mirrors on the ground and you will be urged by the staff to wear this heavy wrap-thing to prevent your panties from being on display.
• ⧫ You have to make sure to reserve your tickets ahead of time. You can order them easily online, but they sell out fast. 
• ⧫ As with many other attractions in Tokyo, it's not good to go on the weekends. The line to get in can be massive.

Venus Fort - A Mysterious and Beautiful Mall in Odaiba

Here's what the interior of the mall looks like.

The location couldn't be better! It's right beside the giant ferris wheel in Odaiba.

Pros:

• ⧫ This mall is massive so it never feels crowded.
• ⧫ There are a wide variety of shops and it seems to have everything you might need (high fashion, fast fashion, toys, furniture, etc.).
• ⧫ They have different projection mapping events that are great to see even if you don't like shopping.
• ⧫ The decor is a spectacle in and of itself.
• ⧫ There are a lot of other interesting things to see and do right beside this mall like taking a ride on the Daikanransha. 
• ⧫ The staff members at the help desk are so friendly and they will gladly help you find the shop that you are looking for. 

Cons:

• ...Honestly I can't think of a single con. Perhaps if you hate shopping malls it won't be your cup of tea, but I personally think it's a fabulous place to check out!!

Sweets Forest - A Paradise for Your Sweet Tooth in Jiyugaoka

You'll feel a bit like you've jumped down the rabbit hole into Wonderland.

The desserts are both cute and delicious!

Pros:

• ⧫ It feels like Harajuku, but you don't have to deal with massive crowds.
• ⧫ All of the sections within the forest have different themes and sweets.
• ⧫ It's a very fun place to go for themed goods during Christmas or Halloween.
• ⧫ You can eat at the forest or you can get the sweets to go.
• ⧫ It's a perfect place for taking "kawaii" pictures for Instagram.
• ⧫ The walk from Jiyugaoka station to this place is very beautiful. Lots of nature and other things to see and do.

Cons:

• ⧫ It doesn't take too long to walk through so it's not a place where you could be for the whole day.
• ⧫ There isn't anything else to do inside of the forest other than eat sweets and take pictures.  

Bourbon Road - A Small Bar Street That Feels Like Old Tokyo

The street looks perfectly staged for a film.

This road comes to life at nighttime.

Pros:

• ⧫ It's really close to Kamata station. 
• ⧫ You can experience a very different side of Tokyo.
• ⧫ If you are interested in places like Golden Gai, go here instead! It's cheaper, less crowded, and friendlier to foreigners.
• ⧫ A lot of the bars have interesting themes.
• ⧫ The food in a lot of these bars is actually really good!

Cons:

• ⧫ Sometimes it's hard to find a bar to sit in as some of the bars only have space for about four or five customers. 
• ⧫ It's difficult to enjoy the experience to its fullest if you don't speak Japanese. Many of the bars don't have English menus and the people working there don't speak English.
• ⧫ If you don't drink alcohol this place might be a little dull for you. 

Oedo Onsen Monogatari - A Great Onsen for First-Timers with an Edo-era Twist

It will make you feel as if you've gone back in time.

A great place to enjoy with friends or family.

Pros:

• ⧫ It's a really good place for foreigners who have never entered a Japanese hot spring. 
• ⧫ There are many things apart from the baths that you can enjoy with your friends or family.
• ⧫ There are instructions in English everywhere so you'll never feel like you don't know what to do. 
• ⧫ The spa treatments are insanely good. I really recommend the body scrub.
• ⧫ They have a lot of delicious festival foods in the cafeteria area. 
• ⧫ Once you are in the onsen, you will use your bracelet to pay for food, treatments, etc., so you don't have to carry cash around with you.
• ⧫ It's a perfect chance to try wearing a yukata.

Cons:

• ⧫ Don't go if you have tattoos. They will ask you to leave and you won't get a refund. If your tattoo is really minuscule, you might be able to get away with putting a band-aid over it... but just know it's a risk. 
• ⧫ If you're not comfortable with getting naked in front of others, it might not be worth the money to go. 
• ⧫ If you are into very traditional onsens, this isn't the place for you as you might find it a bit too "kitschy".

Okubo Dori - A Small Slice of South Korea

You will never go hungry when you're in Shin Okubo

Skin Garden is the first pit stop I make when I walk down Okubo Dori.

 

Pros:

• ⧫ All of the Korean goods and foods are authentic.
• ⧫ It's the perfect place if you are interesting in trying K-beauty products. 
• ⧫ The price of most of the goods are comparable to the actual prices in South Korea.
• ⧫ There are a lot of interesting shops selling popular Korean street foods.
• ⧫ You can find a lot of goods from your favorite Korean idols.
• ⧫ You can simply walk down the main street and find plenty of things to see and do.

Cons:

• ⧫ Wow... the crowds. Don't go on the weekend or after school hours because the streets FLOOD with high school girls. 
• ⧫ If you're only interested in experiencing Japanese culture during your visit, you might want to just skip this place. 

  Bondi Cafe - A Brunch Spot with Beach Vibes

You can sit outside and enjoy the sunshine while you eat.

Yummy yummy!

Pros:

• ⧫ This is such a relaxing cafe that's especially perfect for brunch.
• ⧫ The location is prime. It's right beside Yoyogi Park. After you finish eating you can walk straight through the park to Harajuku.
• ⧫ It's nice to enjoy brunch on the sofas outside on a sunshiny day.  

Cons:

• ⧫ You might be waiting for a table for a while if you forgo making a reservation. 
• ⧫ It is a little bit expensive.
• ⧫ For people who are looking for an "authentic Japanese" travel experience, this place isn't for you as it doesn't serve typical Japanese food.

  *BONUS* Anata No Warehouse - A Very Unusual and Unconventional Arcade

Yes... This is an actual arcade.

Beware of the "jump scare" at the entrance.

Pros:

• ⧫ It's interesting to see even if you're not a huge gamer.
• ⧫ There are a lot of classic games that only cost 50 yen.
• ⧫ You can also pay to play ping-pong, billiards, or darts if you're not into video games.  
• ⧫ There are a lot of interesting photo spots.
• ⧫ They have a very wide variety of games to choose from.

Cons:

• ⧫ This arcade is located in Kanagawa, not Tokyo. If you are staying near Shinjuku it might be a bit of a trek to get there. 
• ⧫ Unless you sign up to be a member, you cannot use the ping pong tables and other things on the top floor.