Cleft lip and palate can be associated with coagulopathy. Here, we report the first known case of congenital platelet disorder and von Willebrand disease presenting as prolonged bleeding after cleft lip and palate repair. After identifying the underlying pathology, platelet infusions and aminocaproic acid were given to decrease bleeding from a second surgical procedure. Whole exome sequencing identified a von Willebrand factor gene mutation, an adenine to guanine substitution at the c.475A location. A high index of suspicion should be had for coagulopathy in patients with syndromic cleft lip and palate.