4 Running Courses in Tokyo

1. Imperial Palace. Distance: 5km. It is recommended to start from Hibiya, Sakuradamon or Nijubashimae stations where there are coin lockers. Run anticlockwise.
2. Nakameguro. Distance: 3km. Take East Exit 1 from Nakameguro station and head towards the Tsutaya bookstore and on to the Meguro River.
3. Asakusa. Distance: 4km. From Asakusa station, follow the pavement north along the river. Take the Sakura Bridge across the river and head south. Run past Ushijima Shrine and head towards Tokyo Skytree until taking a right turn when you hit Kome-dori Avenue-West. Once you pass Tokyo Skytree station, turn right to go back to the Sumida River.
4. Rainbow Bridge. Distance: 15km. Cross the rainbow bridge from Daiba station, heading north towards Hamarikyu gardens and then cross the Tsukiji-o bridge. Take a right when you hit Ariake station and circle back to Odaiba.

Reference:
https://www.timeout.com/tokyo/things-to-do/the-most-scenic-jogging-routes-in-tokyo