Background Acute kidney injury (AKI) is a major postoperative morbidity of patients undergoing cardiac surgery and has a negative effect on prognosis. The kidney outcomes after pulmonary endarterectomy (PEA) have not yet been reported; However, several perioperative characteristics of PEA may induce postoperative AKI. The objective of our study was to identify the incidence and risk factors for postoperative AKI and its association with short-term outcomes. Methods This was a single-center, retrospective, observational, cohort study. Assessments of AKI diagnosis was executed based on the Kidney Disease Improving Global Outcomes (KDIGO) criteria. Results A total of 123 consecutive patients who underwent PEA between 2014 and 2018 were included. The incidence of postoperative AKI was 45% in the study population. Stage 3 AKI was associated with worse short-term outcomes and 90-day mortality (p < 0.001, p = 0.002, respectively). The independent predictors of postoperative AKI were the preoperative platelet count (OR 0.992; 95%CI 0.984-0.999; P = 0.022), preoperative hemoglobin concentration (OR 0.969; 95%CI 0.946-0.993; P = 0.01) and deep hypothermic circulatory arrest (DHCA) time (OR 1.197; 95%CI 1.052-1.362; P = 0.006) in the multivariate analysis. Conclusion The incidence of postoperative AKI was relatively high after PEA compared with other types of cardiothoracic surgeries. The preoperative platelet count, preoperative hemoglobin concentration and DHCA duration were modifiable predictors of AKI, and patients may benefit from some low-risk, low-cost perioperative measures.