Purpose Groin complication following vascular surgery occurs in 10-30% of cases and is associated with significant morbidity and mortality. Institutions have published results on sartorius and rectus femoris muscle flaps to cover arterial reconstructions. However, in recent years, the gracilis muscle flaps has emerged as a an alternative technique . To the best of our knowledge, this study is the first head-to-head comparison of sartorius and gracilis muscle flaps. Methodology A prospective study was carried out between January 2019 to December 2023 at Waikato Hospital. Study design was based on the STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) Checklist. Patients undergoing a muscle flap for an elective or emergent indication under Vascular surgery were included. Primary outcomes were wound healing, mortality, length of stay, reintervention, limb and graft salvage. Results There were 25 flaps created during the study period of which 12 patients had a gracilis flap and the with a median follow up was 26 months. In the gracilis group, 11 (92%) patients completely healed, compared to 9 (69%) in the sartorius group (p=0.16). Median time to healing was 53 days in the gracilis group and 60 days in the sartorius group, though this was not significant (HR=0.93 [0.36-2.4]). There was no difference between the two groups in adjusted mortality (HR=0.46 [0.08 – 1.2]). Three (35%) patients needed reintervention, via groin debridement, in the gracilis group, compared to 1 (8%) in the sartorius cohort. There were two major amputations and 1 graft occlusion in the sartorius group, none in the gracilis group. Conclusion The gracilis holds potential as an alternative muscle coverage option for groin complications. In this single-centre cohort inferiority or superiority was not demonstrated, compared to the traditional sartorius flap. Further multi-centre data should be collected to correlate clinical outcomes with perceived benefits of the gracilis flap.