Background COVID-19 pandemic directly or indirectly increases the burden of unintended pregnancy by limiting women’s access to family planning and other reproductive health services. COVID-19 results in extra 15 million unintended pregnancies over a year. Almost all previous studies conducted about unintended pregnancy were before COVID-19 pandemic in Ethiopia. Therefore, the purpose of this study was to assess the prevalence and associated factors of unintended pregnancy during the COVID-19 pandemic among women attending antenatal care in public hospitals of southwest Ethiopia. Methods This study was cross-sectional and conducted among women attending antenatal care at public hospitals of southwest Ethiopia from June 14 to July 14, 2021. Data were collected using a face-to-face interview. Factors associated with unintended pregnancy were analyzed using binary and multiple logistic regressions with an adjusted odds ratio and 95% confidence interval. Finally, the p-value was used as a graded measure of evidence to quantify the degree of significance. Results A total of 405 women participated in this study. The overall prevalence of unintended pregnancy was 19.5% (95% CI: 1.44–6.92) among women attending antenatal care during COVID-19 pandemic. Of which, 50.6% were mistimed and 49.4% unwanted. Urban residence (AOR: 3.1 95% CI: 1.44–6.92) and not being primary decision-maker (AOR: 2.85 95CI: 1.18–6.88) had high significance with unintended pregnancy. Not having ANC in a previous pregnancy (AOR: 3.40; 95% CI: 1.02–11.94) and not being exposed to community education about maternal health care (AOR: 2.36; 95% CI: 1.06–5.27) had medium significance with unintended pregnancy. Conclusion One-fifth of women attending antenatal care had unintended pregnancies during the COVID-19 pandemic. Efforts to scale up women’s decision-making power on family planning services and access to community education are needed to prevent unintended pregnancy.