To identify the mechanisms of control of temporal schedule of nocturnal migratory flights in small songbirds in nature, we studied the time of departure in a medium-distance nocturnal migrant, the European robin, on the Courish Spit (southeastern Baltic coast) using radiotelemetry. Exact measurements of departure time in 100 birds (58 in autumn and 42 in spring) showed no fixed time window of nocturnal departures during Evening Nautical Twilight. Take-offs occurred throughout the night and even during Morning Astronomical and Nautical Twilight Periods. Departure time showed no significant difference between clear skies and overcast conditions, and significantly differed between the seasons. The median departure time shifted significantly towards sunset during shorter nights in spring as compared to autumn. In both seasons (1) European robins initiating flight after short (1–2 days) stopovers showed no significant differences in departure time between individuals with small and large fuel stores at arrival; and (2) departure time was significantly related to stopover duration: the longer the birds stayed, the earlier they departed in relation to sunset. Only in spring and after longest stopovers, all departures occurred within a short time window soon after sunset.