Yoyogi Park is the fifth largest park in Tokyo and is the most centrally located green space for a run. It was the site of the Olympic Village of the 1964 games. There are lovely paths, gardens, and water features in one section of the park, connected by a pedestrian bridge to a section of the park with stadium, outdoor stage, and other facilities. The Meiji Shrine and grounds are also part of the park but is not appropriate for runners. The paved path is ~1 mile around and the perimeter dirt paths are ~2 miles. Another highlight for runners is the Nohara by Mizuno, right near the park at the Meijijingu-Mae Station. In addition to changing facilities for a modest fee, Nohara includes a studio, run and fitness station, café and kitchen, and a shop. There are running clinics and group runs from here.
Longer Run: Can be combined with Meiji Gaien Park and Akasaka PalaceCombination Yoyogi Park/Meiji Gaien Park/Akasaka Palace: 7 miles