Patients with Ehlers-Danlos syndrome (EDS) are at elevated risk for soft tissue complications when undergoing decompression with or without fusion of the craniocervical junction. We have previously shown that muscle flap closure can decrease reoperative rates. This study investigated whether myofascial flap closure improved clinical outcomes after simple or complex surgery of the craniocervical junction in EDS patients specifically. We performed a retrospective chart review of EDS patients who had undergone surgery for Chiari malformation at the Weill Cornell Medical Center between 2013 and 2020. Postoperative complications were recorded, including infection, wound dehiscence, seroma, hematoma, hardware removal, cerebrospinal fluid (CSF) leak, reoperation, and pseudomeningocele. Patients were stratified by type of closure and type of surgery. Fisher exact test was used for statistical comparison. Between 2013 and 2020, 62 EDS patients who had surgery of the cervicocranial junction were reviewed. Of these, 31 patients had complex surgery with myofascial flap closure and 22 had simple surgery with traditional closure. The mean age at the time of surgery was 21.3 years. There were no significant differences in wound complications or reoperation rates between the simple surgery and complex surgery groups. In addition, there were no significant differences in complications between complex surgery with flap closure and simple surgery with traditional closure. Our CSF cutaneous fistula rate was 0%, considerably lower than rates reported in the literature, and, in one case, a patient developed a postoperative pseudomeningocele secondary to a dural leak, but the myofascial flap closure prevented its progression. Patients with EDS undergoing surgery of the cervicocranial junction may benefit from myofascial flap closure. Flap closure reduced complications after complex surgery of the craniocervical junction to the level of simple surgery. Our CSF leak rate was exceptionally low and only one patient experienced pseudomeningocele. Myofascial flaps are safe to perform in the EDS cohort and prevented CSF cutaneous fistula formation.