Background Health literacy (HL) is an important maternal factor that is involved in the engagement of a mother and her children with health promotion and preventive activities. Studies have found poor HL in large proportions of the population of both developed and developing countries. This study measures the HL of pregnant women and explores its associated factors. Methods A cross-sectional study was conducted on 382 pregnant women attending antenatal care clinics in Mansoura district, Egypt, using an interviewer-administered questionnaire. The Arabic version of the European Health Literacy Survey Questionnaire-short version (HLS-EU-Q16) was used to assess the HL of the participants. Results The study showed that 79.8% of studied pregnant women had limited HL (34.5% insufficient HL and 45.3% problematic HL), and only 20.2% of them had sufficient HL. Limited HL was independently predicted by unsatisfactory income (OR = 6.9; 95% confidence interval [CI]: 3.2–15.3; P ≤ 0.05), lower than university education (OR = 5.3; 95% CI: 1.6–17.2; P ≤ 0.05), and having unplanned pregnancy (OR = 3.7; 95% CI: 1.6–8.5; P ≤ 0.05). Conclusion The majority of pregnant women in this study had limited HL. It was more frequent among women with lower levels of education, insufficient incomes, and unplanned pregnancies. Antenatal care programs should provide services that respond to the HL level and needs of pregnant women.