Long stretches of sea and desert often interrupt the migration routes of small songbirds, whose fat reserves must be restored before these can be crossed as they provide no opportunity for refuelling. To investigate whether magnetic cues might enable inexperienced migratory birds to recognize a region where they need to replenish their body fat, we caught and held thrush nightingales (Luscinia luscinia) in Sweden just before their first migration and exposed them to a magnetic field simulating that at a migratory stopover in northern Egypt, before the Sahara Desert. We found that this magnetic field stimulated the birds to extend their fat-deposition period, indicating that magnetic cues may help small migratory birds to confront large ecological barriers.