Objective To systematically review the prevalence of depression and anxiety among health care workers in designated hospitals during the COVID-19 pandemic. Methods The Cochrane Library, PubMed, EMbase, Web of Science, CNKI, WanFang Data, VIP, and CBM databases were electronically searched to collect cross-sectional studies on the prevalence of depression and anxiety among health care workers from December 2019 to April 2021. Two reviewers independently screened literature, extracted data, and assessed the risk of bias of the included studies. Meta-analysis was then performed using Stata 14.0 software. Results A total of 21 cross-sectional studies were included, involving 38 372 participants. Meta-analysis results showed that during the COVID-19 epidemic, the prevalence of depression and anxiety among health care workers in designated hospitals were 31.00% (95%CI 0.25 to 0.37) and 44.00% (95%CI 0.34 to 0.53). The results of subgroup analysis showed that individuals of female, married, bachelor degree or above, nurses, junior professional titles, and non-first-line medical staff had higher prevalence of depression and anxiety. Conclusions During the COVID-19 pandemic, the incidence of depression and anxiety among health care workers in designated hospitals remain high. Therefore, more attention should be paid to the mental health of health care workers in designated hospitals. Due to the limited quantity and quality of included studies, more high-quality studies are needed to verify the above conclusions.