Background Postoperative portomesenteric venous thrombosis (PMVT) is a rare but potentially serious complication of gastric surgery. This study analyzed the incidence, characteristics, risk factors, and outcomes of PMVT following gastric surgery. Methods Medical records of patients who underwent gastric surgery between January 2007 and December 2012 were reviewed retrospectively. The risk factors of PMVT were analyzed by a logistic regression analysis with control group matched 1:4 by age, sex, and cancer stage and by a Poisson regression analysis with unmatched control group. The resolution rate of PMVT in 12 months was compared between the treatment group and the nontreatment group. Results The total incidence of PMVT after gastric surgery was 0.67 % (31/4611). Most (54.84 %) PMVT cases were detected within 1 month postoperatively. No accompanying deep vein thrombosis (DVT) was noted. Multivariate comparison with 1:4 matched control showed that combined splenectomy, synchronous malignancy, and intra-abdominal complication were independent risk factors. Advanced stage, combined splenectomy, and synchronous malignancy were independent risk factors in Poisson regression analysis using unmatched controls. The resolution rate of PMVT was not different from patients treated with anticoagulation (n = 6) or antiplatelet therapy (n = 1) and were not significantly different with those of the untreated group [85.7 % (6/7) vs. 82.3 % (14/17), p = 0.935] during 1-year follow up. Conclusions PMVT after gastric surgery was associated with advanced cancer stage, combined splenectomy, and synchronous malignancy, but it was not related to laparoscopy or DVT. Significant differences in the natural course of PMVT were not found between the treatment group and observation group.