Tsukuba Express operates a train from Shinjuku to Tsukuba every 30 minutes. Tickets cost $11 and the journey takes 51 min. Alternatively, JR Bus Kanto operates a bus from Shinjuku to Tsukuba every 30 minutes. Tickets cost $11 and the journey takes 1 h 5 min.
How to get from Shinjuku to Tsukuba
From Higashi-Shinjuku subway to Shin-Okachimachi then train to Tsukuba. 1 h 20 min ¥1441. From Shinjuku(Jr) train to Tokyo Station Yaesu Exit then bus to Tsukuba Center. 1 h 35 min ¥1437. From Shinjuku taxi to Tsukuba. 51 min ¥29847. From Shinjuku drive to Tsukuba. 51 min ¥936.