Background Early initiation of antenatal care (ANC) is critical in identifying and mitigating adverse pregnancy-related complications. However, globally, a high percentage of women initiate ANC only at a late stage of their pregnancy. In view of this, the main objective of the study is to establish the prevalence and factors associated with late ANC initiation among women in Malawi. Methods The study was based on the 2015–16 Malawi Demographic and Health Survey (MDHS). The study population consisted of 13,251 women of reproductive age who had given birth during the five years preceding the survey. The data was analyzed using the chi-square test and multivariate logistic regression. Results The prevalence of late ANC initiation in Malawi was 75.6%. The logistic regression modelling revealed increased odds of late ANC initiation attendance among women residing in the Northern Region (AOR: 1.172; 95% CI: 1.021–1.345) and the Central Region (AOR: 1.178; 95% CI: 1.074–1.291), women residing in urban areas (AOR: 1.273; 95% CI: 1.108–1.463), women with no education (AOR: 1.814; 95% CI: 1.13–1.47) or with primary education (AOR: 1.697; 95% CI: 1.13–1.47), women with less than four ANC visits (AOR: 4.155; 95% CI: 4.002–4.814), unmarried women (AOR: 1.478; 95% CI: 1.111–1.985) and those whose last birth was not by caesarean section (AOR: 1.377; 95% CI: 1.179–1.607). Reduced odds of late ANC initiation among women were observed among women in the 20–24 age group (AOR: 0.634; 95% CI: 0.456–0.881), those in the 25–29 age group (AOR: 0.645; 95% CI: 0.476–0.874) and those aged 30–34 years (AOR: 0.634; 95% CI: 0.456–0.881). Conclusions The study found that ANC initiation in Malawi is often delayed, with most first visits occurring after the first trimester. Late ANC initiation is associated with region, place of residence, marital status, and the women’s age. These are significant factors to be considered when designing new or reviewing ANC policies and strategies aimed at increasing ANC utilization and encouraging early initiation of ANC. Earlier ANC initiation among Malawian women can contribute positively towards improving maternal and child health in Malawi. Therefore, government policies and interventions should target women with no or little education, those living in poor families and other modifiable risk factors, such as young unmarried women.