Objective To explore the impact of gender difference in 90-day outcomes after mechanical thrombectomy for acute cerebral infarction. Methods A prospective registration, observational, and retrospective analysis study was carried out. Patients with acute cerebral infarction who were admitted to the Department of Neurology of the First Affiliated Hospital of Chengdu Medical College and the Department of Neurology of Nanjing First Hospital between June 2015 and June 2019 were collected. Patients were divided into two groups based on gender. The detailed demographic, laboratory examination, imaging examination and clinical data were collected. Then, the data were analyzed using univariate and multivariate logistic regression analyses. Results A total of 298 patients were included. Among them, there were 185 males and 113 females. The differences in age, smoking, atrial fibrillation, using antiplatelet drugs before stroke, TOAST classification, and involved cerebrovascular sites between the two groups were statistically significant (P<0.05), and there was no statistically significant difference in other baseline data between the two groups (P>0.05). The results of univariate logistic regression analysis showed that the rate of 90-day favourable outcome of female patients was lower than that of male patients [odds ratio (OR)=0.462, 95% confidence interval (CI) (0.275, 0.775), P=0.030]. The results of multivariate logistic regression analysis showed that, after adjusting for confounding factors, there was no independent correlation between gender and the 90-day favourable outcome of patients with acute cerebral infarction who underwent mechanical thrombectomy [OR=1.511, 95% CI (0.745, 3.066), P=0.253]. Conclusion The gender has no significant effect on the 90-day favourable outcome of acute cerebral infarction patients treated with mechanical thrombectomy.