Naïve migrants reach their wintering grounds following a clock-and-compass strategy. During these inaugural migrations, birds internalise, among others, cues from the Earth's magnetic field to create a geomagnetic map, with which they navigate to destinations familiar to them on subsequent migrations. Geomagnetic map cues are thought to be sensed by a magnetic-particle-based receptor, which can be specifically affected by a magnetic pulse. Indeed, the orientation of experienced but not naïve birds was compromised after magnetic pulsing, indicating geomagnetic map use. Little is known about the importance of this putative magnetoreceptor for navigation and decision-making in free-flying migrants. Therefore, we studied in unprecedented detail how a magnetic pulse would affect departure probability, nocturnal departure timing, departure direction and consistency in flight direction over 50–100 km in experienced and naïve long-distant migrant songbirds using a large-scale radio-tracking system. Contrary to our expectations and despite a high sample size ( n total = 137) for a free-flight study, we found no significant after-effect of the magnetic pulse on the migratory traits, suggesting the geomagnetic map is not essential for the intermediate autumn migration phase. These findings warrant re-thinking about perception and use of geomagnetic maps for migratory decisions within a sensory and ecological context.