Purpose Previous observational epidemiological studies have reported inconsistent findings on the association between dietary intake of omega-3 fatty acids and endocrine-related gynecological cancer such as ovarian cancer and endometrial cancer. This study aimed to investigate this association using a meta-analysis of observational studies. Materials and Methods We searched PubMed, EMBASE, and Cochrane library by using key words related with the topic in April 2017. The pooled odds ratios (pORs), pooled relative risks, or pooled hazard ratios (pHRs) with 95% confidence intervals (CIs) were calculated based on the randomeffects model. Also, we performed subgroup meta-analysis by methodological quality, types of cancer, study design, and omega-3 fatty acids. Results A total of 10 observational studies with six case-control and four cohort studies were included in the final meta-analysis. In the meta-analysis of all the studies, dietary intake of total omega-3 fatty acids was not significantly associated with the risk of endometrial and ovarian cancers (pOR/hazard ratio, 0.87; 95% CI, 0.73 to 1.04; I2=67.2%) (highest vs. lowest intake). In the subgroup meta-analysis by type of study, there was no significant association between them in cohort studies (pHR, 1.03; 95% CI, 0.63 to 1.67; I2=81.9%), whereas its reduced risk was observed in case-control studies (pOR, 0.81; 95% CI, 0.67 to 0.98; I2=55.7%). Conclusion The current meta-analysis of observational studies suggests that there is no higher level of evidence to support the protective effect of dietary omega-3 fatty acids on endocrine-related gynecological cancer. Further prospective studies should be conducted to confirm the association.