Cleft lip with or without cleft palate (CL/P) is the most common congenital craniofacial anomaly with considerable morbidity in affected children. Though extensive studies have established the basic histological and genetic mechanisms of palatal development, the cellular mechanisms that regulate secondary palate development are still not completely understood. Palate fusion is the crucial final step of palate development, in which the medial edge epithelial cells (MEE) make contact to form a midline epithelial seam (MES), which is subsequently removed to allow mesenchymal continuity. Though much progress has been made on understanding the cellular mechanisms of secondary palate fusion, major questions remain in part due to limitations in imaging technologies. Here we utilized new processing and imaging methods to visualize dynamic cell behaviors underlying secondary palate fusion temporally and spatially. We apply these methods to the study of mouse mutants in which apoptosis, or actomyosin contractility have been conditionally disrupted in the secondary palate epithelium. Our results indicate that apoptosis and cell extrusion contribute to MES removal, but that cellular compensation can overcome their loss. Our studies also reveal a unique form of collective epithelial cell migration that is critical for proper completion of secondary palate fusion and suggesting that secondary palate fusion may be a valuable model for understanding how collective epithelial migration occurs in other developmental and disease contexts. Finally, our observations show that genetically ablating actomyosin contractility disrupts MES removal by disrupting collective epithelial cell migration. Overall, our studies suggest a model of compensatory cellular mechanisms in epithelium removal during palate fusion.