Presently, the primary endoscopic options for the treatment of achalasia are peroral endoscopic myotomy (POEM) and pneumatic dilation. But the clinical outcomes of POEM and pneumatic dilation for achalasia have not yet to be fully evaluated. So, we aimed to compare the clinical outcomes between the two treatment modalities. We searched all the relevant studies published up to September 2019 examining the comparative efficacy between POEM and pneumatic dilation. Outcomes included success rate, Eckardt score, lower esophageal sphincter pressure and adverse events. Outcomes were documented by pooled risk ratios and mean difference with 95% confidence interval (CI) using Review Manager 5.3. Seven studies with a total of 619 patients were identified. There were 298 patients underwent POEM treatment and 321 patients underwent pneumatic dilation treatment. The clinical success rate was higher in the POEM group than that in the pneumatic dilation group at 6, 12 and 24 months’ follow-up, with a risk ratio of 1.14 (95% CI, 1.06–1.22, P = 0.0002, I2 = 0%), 1.34 (95% CI, 1.24–1.45, P < 0.00001, I2 = 17%) and 1.35 (95% CI, 1.10–1.65, P = 0.004, I2 = 70%), respectively. The change of Eckardt scores was more obvious in the POEM group than in the pneumatic dilation group, with a mean difference of 1.19 (95% CI, 0.78–1.60, P < 0.00001, I2 = 70%). The rate of gastroesophageal reflux and other complications for POEM was significantly higher than for pneumatic dilation, with a risk ratio of 4.17 (95% CI, 1.52–11.45, P = 0.006, I2 = 61%) and 3.78 (95% CI, 1.41–10.16, P = 0.008, I2 = 0%). Our current evidence suggests that the long-term efficacy of POEM was superior to that of pneumatic dilation, but accompanied by higher complications.