Ampilly-le-Sec is located some 5 km south by south-west of Chatillon-sur-Seine and 15 km east by south-east of Laignes. It can be accessed by the D980 highway from Chatillon-sur-Seine which passes through the village and continues south to Coulmier-le-Sec. The D971 from Buncey to Chamesson also passes through the eastern edge of the commune. From the D971 the D29A goes west through the village then continues to the south-west. The western third of the commune is heavily forested with the rest being entirely farmland.[3]
The Seine River passes through the east of the commune parallel to the D971 flowing from south to north.[3]
The Parish Church of Saint Peter and Paul at Rue de l'Église (1827).[22] The Church contains a large number of items that are registered as historical objects.[22]