The association between coronavirus disease (COVID-19) vaccine acceptance and perceived stigma of having a mental illness is not clear. This study examined the association between COVID-19 vaccine acceptance and perceived stigma among patients with recurrent depressive disorder (depression hereafter) using network analysis. Participants were 1149 depressed patients (842 men, 307 women) who completed survey measures of perceived stigma and COVID-19 vaccine attitudes. T-tests, chi-square tests, and Kruskal–Wallis tests were used to compare differences in demographic and clinical characteristics between depressed patients who indented to accepted vaccines and those who were hesitant. Hierarchical multiple regression analyses assessed the unique association between COVID-19 vaccine acceptance and perceived stigma, independent of depression severity. Network analysis examined item-level relations between COVID-19 vaccine acceptance and perceived stigma after controlling for depressive symptoms. Altogether, 617 depressed patients (53.7%, 95 confidence intervals (CI) %: 50.82–56.58%) reported they would accept future COVID-19 vaccination. Hierarchical multiple regression analyses indicated higher perceived stigma scores predicted lower levels of COVID-19 vaccination acceptance (β = −0.125, P < 0.001), even after controlling for depression severity. In the network model of COVID-19 vaccination acceptance and perceived stigma nodes, “Feel others avoid me because of my illness”, “Feel useless”, and “Feel less competent than I did before” were the most influential symptoms. Furthermore, “COVID-19 vaccination acceptance” had the strongest connections with illness stigma items reflecting social rejection or social isolation concerns (“Employers/co-workers have discriminated”, “Treated with less respect than usual”, “Sense of being unequal in my relationships with others”). Given that a substantial proportion of depressed patients reported hesitancy with accepting COVID-19 vaccines and experiences of mental illness stigma related to social rejection and social isolation, providers working with this group should provide interventions to reduce stigma concerns toward addressing reluctance in receiving COVID-19 vaccines.