Abstract Background Sex differences in clinicopathological characteristics, treatment, and postoperative outcomes of gastric and esophageal cancer are largely undefined. This study aimed to compare tumor and treatment characteristics and outcomes of gastric and esophageal cancer surgery between male and female patients. Methods Patients after elective surgery for primary esophageal (EAC) or gastric adenocarcinoma (GAC) registered in the Dutch Upper GI Cancer Audit between 2011 and 2016 were included. The primary endpoint, 5-year relative survival with relative excess risk (RER), i.e., adjusted for the normal life expectancy, was compared between male and female patients with EAC and GAC. Results In total, 4937 patients were included (75% male) with a mean age of 66 years. cT and cN-stages showed a similar distribution in male and female patients. In females, antrum GAC was more frequent (47% vs. 38%, p < 0.001). Female patients with EAC less frequently received neo-adjuvant treatment (OR = 0.60, 95% CI 0.38–0.96, p = 0.033). For GAC, less postoperative morbidity (33% vs. 38% p = 0.017) and less re-interventions (12% vs. 16%, p = 0.008) were observed in females, although they had inferior 5-year relative survival (49% vs. 56%, RER = 1.31, 95% CI 1.09–1.58, p = 0.004). No differences in relative survival of EAC were observed. Conclusions In addition to significant sex differences in tumor location, female patients with esophageal adenocarcinoma less frequently received neo-adjuvant therapy, and female patients with gastric adenocarcinoma had inferior relative survival. Further consideration and exploration of sex differences in surgical treatment and outcomes are necessary to improve tailored treatment and outcomes.