Background Nearly 90% of deaths from cervical cancer occur in a low resource setting. In Ethiopia, the magnitude of precancerous cervical lesions ranges from 7% to 28%. Precancerous cervical lesions may progress to cervical cancer. Early screening and treatment of precancerous cervical lesions is a cost-effective way to avert the growth of cervical cancer. However, there has been limited research on risk factors for precancerous cervical lesions in Ethiopia. Therefore, this study aimed to identify risk factors for precancerous cervical lesions among women screened for cervical cancer in south Ethiopia. Method A facility-based unmatched case-control study was carried out in five health facilities in south Ethiopia between 8 May to 28 September 2018. Interviewer administered questionnaires were used to collect data from 98 cases and 197 controls. Multivariate logistic regression was employed to identify determinants of precancerous cervical lesions. Results Women aged 30-39 years (AOR = 2.51, 95% CI: 1.03-6.08), monthly income [less than or equal to]66 (AOR = 3.51, 95% CI: 1.77-6.97), initiation of first sexual intercourse at age less than or equal to 20 (AOR = 2.39, 95% CI: 1.14-5.47), having more than one lifetime sexual partner (AOR = 4.70, 95% CI: 2.02-10.95), having a partner/ husband with more than one lifetime sexual partner (AOR = 2.98, 95% CI: 1.35-6.65) had higher odds of precancerous cervical lesions. Conclusion and recommendation Strategies to prevent precancerous cervical lesions should focus on modification of lifestyle and sexual behaviour. The findings of this study highlight several implications for policymakers: targeting older women for cervical cancer screening, addressing inequalities and education relating to risky sexual behaviour may reduce precancerous cervical lesions. Furthermore, future longitudinal studies are needed to assess the awareness of women about cervical cancer screening.