ObjectiveThis study was conducted to assess the determinants of neonatal sepsis in the neonatal intensive care units of public hospitals in Hawassa City Administration, Sidama Region, Ethiopia, in 2020.DesignInstitutional-based, unmatched, case–control study.SettingThe study was conducted in three public hospitals (Hawassa University Teaching Hospital, Adare General Hospital and Hawela Tula Primary Hospital) of Hawassa City, Ethiopia.ParticipantsA total of 331 (110 cases and 221 controls) neonates with their index mothers were included in the study from 1 August to 30 September 2020.Outcome measuresA pretested, interviewer-administered questionnaire and data extraction checklist were used to collect data. Data were coded and entered into EpiData V.3.1 before being exported to SPSS V.20 for analysis. The factors associated with neonatal sepsis were assessed using bivariable and multivariable logistic regression analyses. P value of less than 0.05 was used to establish statistically significant association of variables.ResultsCaesarean section delivery (adjusted OR (AOR)=2.56, 95 % CI 1.3 to 5.00), maternal anaemia (AOR=2.58, 95 % CI 1.45 to 4.6) and lack of vaccination with tetanus toxoid (AOR=3.5, 95% CI 2.07 to 6.19) were all identified as factors significantly associated with neonatal sepsis.ConclusionsCaesarean section delivery, maternal history of anaemia and lack of vaccination with tetanus toxoid were found to be risk factors for neonatal sepsis. Establishing preconception care practice, strengthening the quality of antenatal care and standardising infection prevention practice are needed to improve neonatal health.