Allerey is located some 40 km north-west of Beaune and 30 km north by north-east of Autun. The D906 road passes through the western part of the commune but the village can only be accessed by smaller roads such as the D16 from the south which continues north-east to Arconcey, the D117A from the west which continues south-east to Arnay-le-Duc, and the D36 from Beurey-Bauguay in the north. The commune consists entirely of farmland except for the forested Bois de Come in the south-eastern corner.[3]
The Ruisseau d'Angot rises in the west of the commune and flows south to join the Nailly river.[3]