This pizzeria is located in Shinjuku NEWoMan department store, right outside Shinkuju station - just be sure to take the correct exit!
You can order straight off the menu, or choose from a number of pizza toppings to customise your pizza. The menu changes seasonally, so there's always something new. Once you've been seated and decided on your order, you'll need to make your way up to the counter to order and pay. The staff will make your pizza right in front of you and have it ready to pop into the oven within minutes. Vegetarian options are available.
While you're in the area, I suggest picking up an afternoon snack from Boul'ange, located just minutes away in Shinjuku Southern Terrace.
Pictured: Custom ordered pizza and lemonade
Click on the images to expand.
Suggested access: Shinjuku station.
Address in English: 〒151-0051 Tokyo, Shibuya City, Sendagaya, 5 Chome−24−55 NEWoMan SHINJUKU エキソト2F
Address in Japanese: 〒151-0051 東京都渋谷区千駄ケ谷５丁目２４−55 NEWoMan SHINJUKU エキソト2F
What else can I do in Tokyo?
I wrote about visiting Meiji Shrine, Shibuya Sky, and the Yayoi Kusama Museum in Tokyo, which you can check out here: Finding Peace in Tokyo.
I also recommend checking out Get Your Guide, which has a great selection activities and short tours available all over Japan. They also sell entry tickets to some of Tokyo's most popular tourist attractions. Lastly, I have to recommend one of my favourite travel websites, Trip Advisor. I often use Trip Advisor to check hotel and restaurant ratings when travelling, and usually find it to be quite reliable. Happy travelling!