Introduction To evaluate clinicopathologic features and prognosis of post-complete resection in patients with PDGFRA-mutant gastrointestinal stromal tumor (GIST), and even to establish a relapse-free survival (RFS) prognostic model for this subgroup. Methods This retrospective study used data from patients with primary PDGFRA-mutant GIST who underwent complete resection (2005-2019) at 16 large-scale medical centers in China. Stepwise multivariate Cox regression models were performed to build the prediction model, in which the potential predictors were available in routine clinical practice and using the risk score functions. The prediction model was cross-validated by calibration histogram and time-dependent receiver operating characteristic curves. Results A total of 280 patients with PDGFRA-mutant (172 D842V-mutant and 108 non-D842V-mutant) GIST after complete resection were enrolled. Most tumors originated in the stomach (89.6%). The 1-, 3-, and 5-year RFS rates were 95.9%, 91.2%, and 89.5%, respectively. The RFS of the non-D842V-mutant group was superior to that of the D842V group (P = 0.033). Multivariate analysis demonstrated that D842V mutation (P = 0.017), non-gastric tumor (P < 0.001), and Ki-67 > 5% (P = 0.005) were the independent variables influencing the prognosis of patients with PDGFRA-mutant GIST. The scoring model showed the predicted and actual cumulative 1-, 3- and 5-year follow-up relapse rates fit well. Conclusions PDGFRA-mutant GIST mostly originated in the stomach and had a favorable prognosis after surgery. Non-D842V-mutant patients might have better prognoses than D842V-mutant patients. The prognostic model demonstrated favorable prediction accuracy, suggesting its clinical utility.