Pepe moved joined the oral medicine department at Guy's and St Thomas' in 1989 and became an honorary senior lecturer within the King's College London Dental Institute. She worked part time as a specialist in oral medicine and became a consultant in oral medicine in 2003. She moved into clinical management in 2004 and until very recently worked half her time as a consultant and half as clinical director for the Dental Hospital at Guy's and St Thomas'. She is currently workstream owner for the outpatients transformation workstream.
Pepe was responsible for developing the local anaesthetic allergy testing service. Guy's and St Thomas' is one of the few places within the South East offering this service and has almost reached the status of a regional centre for this, receiving referrals from other allergy clinics as well as local general medical and dental practitioners.