Abstract Background Branchial arch lesions (BALS) are uncommon congenital malformations presenting mainly in first 2 decades with neck cysts, sinuses, fistulas, recurrent infections and have low potential to turn malignant. Surgical management of these lesions can be associated with significant risk of complications and recurrence. Sclerotherapy has been described as effective and less invasive alternative option. Aim of the Study is to summarize current available evidence regarding effectiveness and safety of surgery and sclerotherapy as two modalities of treatment for BALS. Methods A systematic review for all interventional studies on management of (BALS) was conducted in multiple medical databases from its inception till March 2021 with inclusion of all studies reporting on either surgical management or sclerotherapy for BALS in humans and reported effectiveness or safety outcomes. Diagnostic and review articles, single case reports and non-human studies were excluded. Proportional meta-analyses were utilized where there is only uncontrolled studies available reporting on outcomes. Assessment of quality was done with use of validated tool relevant to design of primary studies included and risk of bias of studies was assessed statistically. PRISMA Guidelines were followed in reporting of the study. Results A total of 525 studies were retrieved of which only 25 were eligible for inclusion. All included studies were uncontrolled case series; 18 reported on surgery and 7 reported on sclerotherapy The overall quality of included studies were fair to good according to NIH validated tool. Meta-analyses of surgical studies for BALS showed success rate of complete excision of 90%,96%,96% and 98% for first, second, third and fourth branchial arch lesions respectively with complications rates of 19.7%,5%,24% for first, second and third arch lesions. The rates of recurrence were 11.2%,2%,5%,1% for first to fourth arch lesions in order. The corresponding success rates of completed resolution for sclerotherapy were 86% with complications rates of 8% all of which were minor complications. There were no recurrences but recognized incomplete resolution. Conclusion Both surgery and sclerotherapy have satisfactory success in terms of complete excision/resolution of BALS. The risks of complications howeverseem to be more significant with surgical management however no controlled studies were available to allow for definitive conclusions. Further studies with standardized diagnostic criteria and treatment techniquesare needed to allow for prioritizing treatment lines based on conclusive evidence.