Free flap reconstruction is the standard method for reconstructing large maxillary defects. Palatal fistula is an uncommon complication following reconstructive surgery. This study aims to describe the incidence, etiology, and management of palatal fistulae following reconstruction of oncological maxillectomy defects. A total of 108 patients from a single institution who underwent maxillectomy surgery between 2008 and 2014 were retrospectively reviewed. Ninety-two patients had resection of the hard palate. Sixty-eight patients underwent immediate free flap reconstruction of the palate; 55 had reconstruction of the hard palate with skin, and thirteen had reconstruction of the hard palate with muscle. The incidence of palatal fistulae in the reconstructed palates was 12% (11 patients) in this series: five after muscular reconstruction of the hard palate and six after cutaneous reconstruction. Muscular reconstruction of the hard palate is associated with a significantly higher incidence of palatal fistulae compared with cutaneous reconstruction (p = 0.015). The Cordeiro classification, smoking, diabetes, immunosuppression, and radiotherapy were not significant risk factors (p > 0.05). Based on our experience, we caution against attempting direct closure for established palatal fistulae, the majority of patients who had attempted direct closure of their fistulae failed to achieve resolution.