Waterperry with Thomley is a civil parish in the South Oxfordshire district, in the county of Oxfordshire, England. It includes the village of Waterperry (Ordnance Survey grid reference SP626066) and the abandoned former village of Thomley (OS Grid ref. SP629091). It had a population of 257 recorded in the United Kingdom Census 2011. The area is bisected by the M40 motorway, it is in the valley of the Thame and centred approximately 7 miles (11 km) east of the city of Oxford.

The parish was formed on 1 April 1994 from "Waterperry" and "Thomley".