Achalasia is a rare esophageal motility disorder characterized by impaired relaxation of the lower esophageal sphincter (LES) and absence of peristalsis, leading to significant swallowing difficulties and other symptoms. Traditional treatment options, including Heller myotomy (HM) and pneumatic dilation (PD), have been effective but are associated with risks such as perforation and gastroesophageal reflux disease (GERD). Peroral endoscopic myotomy (POEM) has emerged as a minimally invasive alternative, potentially offering several advantages over conventional methods. This systematic review aims to compare the efficacy, safety, and long-term outcomes of POEM versus HM in the treatment of achalasia. We systematically reviewed studies that compared POEM with HM in achalasia patients, focusing on key outcomes such as myotomy length, operative time, treatment success rates, and complication rates. The review included 15 studies comprising four randomized controlled trials, 10 cohort studies, and one case-control study. The results consistently showed that POEM achieved longer myotomy lengths and shorter operative times compared to HM. POEM also demonstrated higher or comparable treatment success rates, with a uniform definition of success based on achieving an Eckardt score of ≤3. However, the complication rates, particularly the incidence of GERD, varied between the two procedures, highlighting the need for careful patient selection and long-term follow-up. POEM offers a promising alternative to HM for the treatment of achalasia, with advantages in terms of reduced invasiveness, shorter operative times, and potentially higher treatment success rates. However, further high-quality research is necessary to fully establish its long-term efficacy and safety compared to conventional treatments.