Background and Objectives: Investigating the level of anxiety and suicidal thoughts in nurses during the COVID-19 pandemic can play an important role in helping them clinically to prevent the development of psychological symptoms in them. In this regard, this study aims to investigate the prevalence of anxiety and suicidal ideation in nurses working in COVID-19 wards compared to nurses from other departments. Methods: In this analytical cross-sectional study, participants were 347 nurses from two hospitals (Shahid Beheshti and Kamkar) in Qom, Iran in 2021. Nurses were divided into two groups working in COVID-19 and non-COVID wards. The data collection tools were a demographic form, Beck’s anxiety inventory, and the Beck scale for suicidal ideation. The data was analyzed in SPSS software version 22 using independent t-test or ANOVA for quantitative data and chi-square test for qualitative data. The significance level was set at 0.05. Results: Among participants, 139(40.1%) were in the COVID group and 208(59.9%) were in the non-COVID group. Nurses in the COVID group had significantly higher anxiety scores than nurses in the non-COVID group (P<0.001), but there was no significant difference between COVID and non-COVID groups in suicidal ideation (P=0.979). Conclusion: There is a high prevalence of anxiety among nurses working in COVID-19 wards compared to nurses from other wards. Therefore, it is recommended to use psychological treatments to reduce the anxiety and suicidal thoughts of these nurses during the COVID-19 pandemic.