Tokyo is very busy, and it is not easy and safe to run, particularly for international tourists. There are, however, some good area for jogging. If you are a big runner, wanting to jog a long distance in a safe space during your stay in Tokyo, it might be a good idea to find a hotel near by the following jogging routes.
Close to Tokyo train station, this is one of the most popular tourist spots in Tokyo, and a very popular jogging spot at the same time, particularly in early and after work hours. With many jogging clubs running together, this 5km circle course is so popular and busy that it sometimes looks a marathon race ! If you want to avoid the crowd, very early morning or middle of the day would be the best time.
There are many hotels in this area. Particularly the west side of Imperial Palace is more reasonably priced (the east side is Tokyo station area and expensive).
If you prefer to enjoy more relaxing jogging in green area, Yoyogi Park is a great place. Close to Harajyuku/Shibuya stations, there are many small paths to jog around in this park (a full circle is about 3km).
Yogyogi park is big and free to enter. Some hotels are within running distance.
This is the sports complex area (including Japan National Stadium and Tokyo Metropolitan Gymnasium), and popular for joggers as the path is relatively wide and easy. In autumn season, the leaf of tree changes and the whole street becomes very beautiful.
This is quiet area in busy Tokyo and there are stadiums for baseball and Rugby (good if you are planning to watch the game). There are some hotels in this area.