This protocol outlines a systematic review and meta-analysis aimed at evaluating the efficacy and safety of various surgical techniques for treating hypothalamic hamartomas (HHs), which are congenital lesions causing pharmacoresistant epilepsy and severe neuropsychological impairment. Despite the availability of multiple surgical approaches, there is a lack of direct comparison in the literature regarding their outcomes. The review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Individual Participant Data (PRISMA-IPD) guidelines, searching three major databases (PubMed, Embase, and Scopus) without language restrictions. The process involves screening for eligible articles by two independent reviewers, with a third resolving conflicts, and includes both study-level and individual patient data (IPD) analyses. The study-level analysis will assess heterogeneity and quantify seizure outcomes, while the IPD analysis will identify predictors of seizure freedom and postoperative complications to aid in selecting the appropriate patient and surgical technique. This research, which does not require ethics approval as it relies on existing data, aims to fill a significant gap in the literature and will be disseminated through conferences and neurosurgical journals. Registration number: CRD42022378876.