Background In recent years, there were great controversies about gender disparities in stroke outcome. The study was aimed to investigate sex differences in stroke case fatality on all published studies based in a comprehensive meta-analysis. Methods A systematic search of Pubmed, EMBASE, SCOPUS, ISI Web of Science, and Cochrane Library was conducted for the included papers between 1992 and 2009. For the pooled group and subgroup analysis, fixed effects or random effects model were used to find sex differences in case fatality of stroke with a Mantel-Haenszel method. Meta-regression analysis was performed to study methodological heterogeneity. Results Thirty-six population-based studies, together with three randomized clinical trials (RCTs), were included in the present study. For the pooled group, there was an overall hazard risk of 1.13 for women compared with men. A hazard risk of 1.27 was observed for women in RCTs subgroup and 1.12 for women in population-based subgroup. The regression analysis found no significant correlation between methodological variables and heterogeneity. Conclusions Due to the limited data about sex differences in stroke case fatality, the findings should be treated cautiously as preliminary. More large multicenter clinical trials should be performed to verify the reliability of the results.