To investigate the association between tumor laterality and prognosis across different histological subtypes of ovarian cancer. In this study, we enrolled patients with ovarian serous cancer (SC), endometrioid cancer (EC), mucinous cancer (MC), clear cell cancer (CCC), sex cord-stromal tumor (SCST) and malignant germ cell tumor (MGCT) from the Surveillance, Epidemiology, and End Results (SEER) database between 1988 and 2017. Additionally, we enrolled MGCT patients from a Chinese multi-institutional registry between 2003 and 2020 for complementary analyses. The primary outcomes were cancer-specific survival (CSS) and disease-free survival (DFS) in the SEER cohort and Chinese cohort, respectively. Multivariate Cox regression and Kaplan-Meier analyses were used to assess the association of tumor laterality with prognosis. In the SEER cohort with 13597 ovarian cancer patients, the fully-adjusted multivariate Cox regression model showed the right-sided tumor was significantly associated with a better CSS than the left-sided tumor (hazard ratio [HR] 0.51, 95 % confidence interval [CI]: 0.27-0.97; P = 0.041) among MGCT patients, whereas no significant association between tumor laterality and CSS was found among patients with SC, EC, MC, CCC and SCST (all P > 0.05). Furthermore, among the 288 MGCT patients in the Chinese cohort, the significant association of right-sided disease with better DFS (HR: 0.18, 95 % CI: 0.05-0.68; P = 0.011) was also observed. Similar results were found in the Kaplan-Meier analyses. Patients with right-sided tumor had a better prognosis than those with left-sided tumor in MGCT, but not in other ovarian cancer subtypes. Our findings suggested that personalized treatment strategies based on the tumor laterality might be necessary among MGCT patients.