The Institute is headquartered in the Old Road Campus Research Building (ORCRB) of the University of Oxford in purpose built new laboratories.

As well as providing central facilities at the Jenner Institute Laboratories (located in the Nuffield Department of Medicine) in Headington and the Jenner Building in Compton, the Institute, through the support of many funders, supports Investigators and their research at multiple sites. These include the Weatherall Institute of Molecular Medicine, the Centre for Clinical Vaccinology and Tropical Medicine, the Institute for Animal Health's Pirbright site, the Medawar Building for Pathogen Research and the Sir William Dunn School of Pathology.

A number of vaccines being developed by Jenner Investigators are manufactured to GMP clinical grade at the University's Clinical Biomanufacturing Facility.