Background: The incidence and risk factors of chronic thromboembolic pulmonary hypertension (CTEPH) after acute pulmonary embolism (PE) were still controversial. A systematic review and meta-analysis was conducted to assess the incidence and risk factors of CTEPH after acute PE. Methods: Embase, Medline, China National Knowledge Infrastructure, Wanfang databases, and various reference lists were searched to identify studies published up to May 2018. Only cohort studies that used right heart catheterization for CTEPH diagnosis were included. The study quality was assessed using the Newcastle-Ottawa Scale (NOS). All analyses were conducted with the meta package in R software (3.2.2). Results: Fifteen studies met the inclusion criteria. The overall incidence of CTEPH after acute PE, with a median follow-up from 6 to 94.3 months, was 3.13% (95% CI: 2.11-4.63%). The incidence of studies from China [4.46% (95% CI: 1.68-11.32%)] was slightly higher than from Europe [2.82% (95% CI: 1.82-4.34%)]. However, there was no significant difference between these two groups (P=0.39). Subgroup analyses of confirmed diagnostic method showed that compared studies using right heart catheterization [3.25% (95% CI: 2.12-4.97%)], studies using right heart catheterization combined with bundled tests tended to yield a similar data [2.40% (95% CI: 0.97-5.81%), P=0.54]. Previous/recurrent PE or previous VTE, idiopathic PE and right heart dysfunction were considered as risk factors of CTEPH in patients with a previous PE. Conclusions: CTEPH is not a rare complication of acute PE. Close follow-up and implementation of a comprehensive screening program are important, especially in patients with independent risk factors.