Given the sets of flights and aircraft of an airline carrier, the fleet assignment problem consists of assigning the most profitable aircraft type to each flight. In this paper we propose a model for the periodic fleet assignment problem with time windows in which departure times are also determined. Anticipated profits depend on the schedule and the selection of aircraft types. In addition, short spacings between consecutive flights which serve the same origin-destination pair of airports are penalized. We propose a non-linear integer multi-commodity network flow formulation. We develop new branch-and-bound strategies which are embedded in our branch-and-price solution strategy. Finally, we present computational results for periodic daily schedules on three real-world data sets.