Plan your movements well. Even the cheapest way of transportation in Tokyo (the JR East urban railway) will become quite expensive if you keep going in and out of the stations several times a day. To cut down on expenses, organize your sightseeing and shopping to visit places in the same area in a single day, so you don’t need to repeat the same trip again.
Take advantage of the many free attractions offered in Tokyo. If you’re coming in spring, city parks will be blooming with cherry trees and offer great opportunities for hiking and photography. The tallest building in Tokyo and the best observation deck, at the top of the Shinjuku’s twin tower office building, are free. The same is true of areas such as Asakusa (great for shopping), Harajuku (to watch post-modernist street fashion) and Akihabura Electric Town (wide array of electronics in thousands of shops).
Shop for souvenirs at the 100 Yen Shop (the Japanese equivalent to the dollar store in the United States), which offer a wide array of items, from cups with Kanji writings to flags, magnets, chopsticks, bath salts and other great finds. Many of the items here are actually quite similar to the ones you would find at expensive souvenir shops.
Visit during the low season. This means avoiding Tokyo during the period around New Year and major holidays (late April and mid-August). Summer tends to be cheaper, as many locals head out of the city for their own holidays and hotels and restaurants offer specials in hopes of attracting customers.
Buy your food from street vendors or window restaurants. Japan is one of the few countries where this is perfectly safe, so take advantage of that. If you stick to traditional food (noodles, soups or sushi), your food budget will be reduced to almost nothing. If you miss Western food, fast food places such as McDonald's might be a better choice than Western sit-down restaurants.