The exact anatomical location for an iron particle-based magnetic sense remains enigmatic in vertebrates. For mammals, findings from a cornea anaesthesia experiment in mole rats suggest that it carries the primary sensors for magnetoreception. Yet, this has never been tested in a free-ranging mammal. Here, we investigated whether intact corneal sensation is crucial for navigation in migrating Nathusius' bats, Pipistrellus nathusii, translocated from their migratory corridor. We found that bats treated with corneal anaesthesia in both eyes flew in random directions after translocation and release, contrasting bats with a single eye treated, and the control group, which both oriented in the seasonally appropriate direction. Using a Y-maze test, we confirmed that light detection remained unaffected by topical anaesthesia. Therefore our results suggest the cornea as a possible site of magnetoreception in bats, although other conceivable effects of the anaesthetic are also explored. Furthermore, we demonstrate that the corneal based sense is of bilateral nature but can function in a single eye if necessary.