Introduction: Hypertrophic cardiomyopathy (HCM) is a genetic disorder characterized by asymmetric hypertrophy of the myocardium, often resulting in left ventricular outflow tract (LVOT) obstruction. This condition affects approximately 1 in 500 individuals in the general population and is one of the leading causes of sudden death in young people. Surgical treatment is indicated when clinical management fails to relieve symptoms and reduce the risk of adverse events. The two main surgical approaches for obstructive HCM are septoplasty and transaortic myomectomy, aiming to improve blood flow and reduce the intraventricular gradient. However, there is disagreement in the literature regarding which technique offers better long-term outcomes. Objective: The study aims to compare the surgical outcomes of septoplasty and transaortic myomectomy in patients with obstructive hypertrophic cardiomyopathy, evaluating the efficacy of both techniques in reducing symptoms, relieving LVOT obstruction, incidence of postoperative complications, and long-term survival. Methodology: A systematic review was conducted following PRISMA guidelines, with a search in PubMed, Embase, Scopus, Web of Science, and Cochrane Library databases, covering January 2000 to September 2024. Randomized studies, cohorts, and case series that directly compared septoplasty and transaortic myomectomy in patients with obstructive HCM were included. Exclusion criteria included studies that did not directly compare the two techniques, isolated case reports, and narrative reviews. Two independent reviewers conducted study selection, with a third reviewer resolving any discrepancies. Results: Septoplasty showed greater efficacy in reducing symptoms and left ventricular outflow gradient, and was associated with a lower risk of immediate complications such as infection and the need for reoperation. Transaortic myomectomy, while also effective, was associated with a slightly higher risk of surgical complications, particularly in cases of complex septal anatomy. Both procedures showed comparable operative mortality rates, but septoplasty demonstrated better long-term outcomes in terms of survival and preservation of cardiac function. Conclusion: Both septoplasty and transaortic myomectomy are effective techniques for the treatment of obstructive HCM, with septoplasty being preferred due to its lower morbidity profile and better long-term outcomes. However, transaortic myomectomy may be indicated in cases of extensive septal hypertrophy or complex anatomy. Surgical decisions should be individualized, taking into account patient characteristics and the surgical team's experience. Future studies are needed to evaluate the nuances of long-term outcomes in different patient populations.