Timely entries to antenatal care have various benefits for pregnant women and birth outcomes. The aim of antenatal care is to assure that every pregnancy culminates in the delivery of a healthy baby without negative effects on the health of pregnant women through health promotion and disease prevention, early detection, and treatment of complications and existing diseases. Hence, this study assessed the late initiation of antenatal care and associated factors among pregnant women attending antenatal clinics at public health centers of Ilu Ababor Zone, southwest Ethiopia. An Institution-based cross-sectional study was carried out among 389 pregnant women who were attending antenatal care service at twelve randomly selected health centers. A systematic sampling technique was employed to recruit pregnant women. Pretested and structured questionnaires were used to collect data. Data were entered into Epidata and exported to SPSS for analysis. Those women who started antenatal care follow up after 12 weeks of gestational age were categorized as booked lately. Bivariable and multivariable logistic regression was employed to identify an association between the independent predictors and the outcome variable. In this study, 277 (71.2%) of the participants were booked their first antenatal care visit lately. Having family size of ≥ 4 (AOR: 2.25; 95% CI: 1.07–4.74), maternal age ≥ 25 years (AOR: 2.30; 95%CI: 1.02–5.18) and perceived the right time of booking > 12 weeks of gestation (AOR: 2.39; 95% CI: 1.13–5.04) had higher odds of late antenatal care initiation. Similarly, not being a member of women’s health developmental army (AOR: 2.35; 95%CI: 1.09–5.07) and ANC not attended previously (AOR: 3.32; 95% CI: 1.17–9.42) had also a more likelihood of booking antenatal care lately. In this study, the majority of women started antenatal care lately. Thus, the provision of health education on the importance of attending first antenatal care early is recommended.