Seibu Railways operates a train from Fussa to Shinjuku hourly. Tickets cost $5 - $8 and the journey takes 48 min. Japan Railways (JR) also services this route every 30 minutes.
How to get from Fussa to Shinjuku
From Haijima train to Seibu-Shinjuku. 48 min ¥727. From Haijima train to Tachikawa then train to Shinjuku(Jr). 49 min ¥720. From Fussa taxi to Shinjuku. 37 min ¥17838. From Fussa drive to Shinjuku. 37 min ¥556.