Background This study retrospectively compared the safety and efficacy of two endoscopic techniques for treating newly diagnosed achalasia, pneumatic dilation (PD), and peroral endoscopic myotomy (POEM). Methods Demographics, clinical and manometric data, and outcomes were collected from the medical records of patients who received POEM or PD as the primary therapy for achalasia at our hospital from January 2012 to August 2015. Results Of 72 patients, 32 and 40 received POEM and PD, respectively. The two groups had similar preoperative features. On short-term follow-up, improvements in high-resolution esophageal manometry and barium esophagogram parameters were similar. For PD, the success rates at 3, 6, 12, 24, and 36 months were 95, 88, 75, 72, and 60%, respectively. For POEM, these were 96, 96, 96, 93, and 93% (P = 0.013, log-rank test). On subgroup analysis, the success rate was higher with POEM than that with PD in all 3 manometric subtypes, but only that of type III was statistically significant. POEM required significantly longer operative time and hospitalization than did PD (P < 0.001). Four POEM patients experienced subcutaneous emphysema. The rate of gastroesophageal reflux was higher in patients treated by POEM (18.8%) than that in PD (10%; P = 0.286). Conclusions In the intermediate term, the remission rate of symptoms associated with POEM therapy was better than that with PD for newly diagnosed achalasia, especially in patients with type III achalasia. The short-term outcomes of the two therapies were similar.