The headquarters dojo of Sengenkan is located in the Shinjuku Ward of Tokyo, across the street from the Ochiai stations of the Tozai subway line. The dojo occupies the entire 3rd floor of the Takayama Main Building ("Takayama Honkan"). The property was formerly the Tsukimigaoka Hachmangu shrine. The shrine was renamed as "Sengen-jinja" in 2010 and still exist in the back courtyard of the property. 

The dojo boasts a training area of 150 tatami mats (approximately 300m2) making it the largest Aikido training hall in Tokyo. There is an entrance hall, main administration office, small lounge, large lounge, separate make and female changing rooms with lockers and showers, a small kitchen, and some other amenity rooms. The main dojo of 150 mats is an airy, spacing area with many windows and a wall-size mirror, with rafters to hang dogis. There is also a small dojo of 50 mats, that can be used for training, but is also used for cultural activities such as tea ceremony (chado) and calligraphy (shuuji), and can even be used as sleeping quarter for visitors attending training camps.