As the largest centre for Japanese studies in the UK, SOAS is an invaluable partner for the Sainsbury Institute. The relationship is formalized by the membership of the Director and Principal of SOAS of the Institute's Management Board. The London Office of the Institute operates under the auspices of the Faculty of Arts and Humanities, and works in close cooperation with staff in the Department of Art and Archaeology.

The Institute also collaborates with the School's Japan Research Centre, which serves as a national and international centre for Japanese studies, and which maintains links with Japanese scholars, Japanese universities and the Japanese community in London. The Institute maintains its London offices in the Brunei Gallery, where the Department of Art and Archaeology is based. John T. Carpenter, Reader in the History of Japanese Art at SOAS, has served as the Head of the London Office for the past nine years. The Institute entered into a new institutional agreement with SOAS for 2008-2011. It covers library support, use of SOAS office space and facilities by Sainsbury Institute research fellows and staff, the role of the Head of the Institute's London Office at SOAS, and collaborative research projects.

The London office provides study space for Robert and Lisa Sainsbury Fellows in the Handa Study Room on the fourth floor of the Brunei Gallery building, and regularly hosts visiting scholars on a temporary basis in B401 on the same floor.