The medieval and early modern manuscripts owned by Jesus College date back to the 11th century. They have been on deposit in the Bodleian Libraries since 1886 and thus appointments to consult manuscripts with numbers between 1 and 150 should be made at the Weston Library.

The most recent catalogue is the second volume of Coxe's Catalogus codicum MSS. qui in collegiis aulisque Oxoniensibus hodie adservantur (1852); entries for pre-1601 manuscripts are also available at Medieval.Bodleian. An annotated version of Coxe's catalogue is held in the Library Office. (MS 146 is catalogued in Ker's Medieval manuscripts in British libraries.) Modern manuscripts numbered 151 and above, including T.E. Lawrence's undergraduate thesis (MS 181), are held in the College Library and the Archives.