The Henry Martyn Trust was established in 1881, a time of great enthusiasm in Cambridge for overseas missions, by Revd John B___, vicar of Holy Trinity and previously a missionary to India. It first built the Henry Martyn Hall (1887) as a meeting place for the promotion of mission.  In 1897 an appeal was launched for a 'Proposed Missionary Library for Cambridge University', to be housed in the Hall. The ambitious stated purpose of the Library was to 'give students access to the best material' and 'help build up a true sense of the importance of Missions in those who will afterwards hold the highest offices both in Church and State'.

The Henry Martyn Library opened in the Hall in 1898, and there it remained as a small collection of missionary biographies and other books until 1995. The evolution of the Henry Martyn Library into the present Henry Martyn Centre began in 1992, when Canon Graham Kings, now Bishop of Sherbourne, was appointed as the first Henry Martyn Lecturer in Missiology in the Cambridge Theological Federation.

During the 1990's the Library became the focus in Cambridge for the rapidly developing academic study of mission and world Christianity.

In its centenary year of 1998, the library adopted the new title, 'Henry Martyn Centre' in recognition of the widening field of scholarly activity in which its Director and staff were now engaged. In 1999 the Centre became an Associate Institute of the Cambridge Theological Federation, one of the largest providers of theological education in the United Kingdom. Prof Sebastian Kim, Ripon and York St John University, was interim director of the centre between 2000-2001 and Prof Brian Stanley of University of Edinburgh was director between 2001 -2010.

Today, the Centre continues to seek to promote the study of mission and world Christianity, developing strong links with mission study centres around the world and fulfilling the same aim that was stated by the founders of the Library in 1897. Since 2010 all the activities of the Trust take place at the Centre in Westminster College and the Hall is leased to Holy Trinity Church.