First of all, I am glad to know that you have decided to find a relatively long-term accommodation space in Tokyo. It’s a marvelous city and I hope you will have a fantastic time living here ~ The ideal procedure would be to lookup apartments in your desired area on these websites and then go an agency. Most apartments won’t be furnished and will have the initial surcharges and key deposit money, ~one month’s rent. The agency I used for my apartment is ABLE, and I would highly recommend it. I have a contact at ABLE Hakusan, so if you are looking for housing in Bunkyo-ku, near the universities, ping me up and I may perhaps be able to get you a bit of a discount, haha ;) Some relevant links are, https://suumo.jp/sp/ : This is the largest real-estate website in Japan, with the most number of properties listed. Most of the information is in Japanese though. https://minimini.jp/sp/ : The second most popular real-estate website in the country. Suumo is Green, while MiniMini is Red. Both of