Background Cutaneous squamous cell carcinomas (cSCC) occur predominantly on sun-exposed areas of the body. Surgical excision with adequate margins is considered curative, however lesions on the head and neck are very high-risk for incomplete and close margin excision due to involvement of complex anatomical structures. Methods A retrospective review of 435 head and neck cSCC excisions performed between 2016–2020 at the Royal Hobart Hospital, Tasmania, was conducted. Variables included operative location (main theatre vs day procedure unit) and anaesthetic modality. Incomplete margins were defined as tumour at any margin; close margins as less than 1 mm. Statistical analyses included logistic regression and t-tests. Results 435 head and neck cSCC were identified. 11.5% of lesions were incompletely excised, and 10.5% with close margins. Increased risk of incomplete excision and close margin excision were observed in scalp location, moderately and poorly differentiated cSCC, the presence of perineural or lymphovascular invasion, and lesions with increased diameter and depth of invasion. Excisions performed under only local anaesthetics showed a reduction in rates of close excision, and no other statistical significant differences were demonstrated in comparison of surgeon seniority and operative location. Conclusion The study reports features of head and neck cSCC contributing to increased risks of incomplete and close margin excision. Recognizing these risk factors preoperatively can inform surgical planning and improve outcomes.