Background: Antenatal care coverage is very low in low-and middle-income countries, including Ethiopia. Self-reported pregnant women’s satisfaction may be important in identifying the demographic, provider-, and facility-related factors that can be improved to increase antenatal care satisfaction. However, there is a paucity of data on pregnant women’s satisfaction in Ethiopia, particularly in the study setting. Therefore, this study aimed to assess antenatal care service satisfaction and associated factors among pregnant women at public health facilities in the Harari region of eastern Ethiopia. Methods: A health institution–based cross-sectional study was conducted among women who were attending antenatal care clinics in February 2017. All 531 pregnant women were selected using a systematic random sampling method. Data were collected using an interviewer-administered questionnaire, entered into EpiData version 3.1, and analyzed using SPSS version 22.0 software. A logistic regression model was applied to control for confounders. The level of significance was determined at a p-value of less than 0.05. Results: The magnitude of pregnant women’s satisfaction with antenatal care services was 70.3% (95% confidence interval (CI) = 66.4%–74.3%). Receiving antenatal care services from the hospital (adjusted odds ratio (AOR) = 2.44, 95% CI = 1.50–3.98), did not attend formal education (AOR = 2.53, 95% CI = 1.52–4.20) and attended primary education (AOR = 2.17, 95% CI = 1.17–4.04), having a repeated visit to antenatal care (AOR = 4.62, 95% CI = 2.98–7.17), initiating antenatal care services within the first trimester (AOR = 1.74, 95% CI = 1.12–2.71), having no history of stillbirth (AOR = 2.52, 95% CI = 1.37–4.65), and waiting for no more than 30 min in the health facility to get service (AOR = 2.31, 95% CI = 1.28–4.16) were factors associated with pregnant women’s satisfaction with antenatal care services. Conclusion: More than two-thirds of pregnant women were satisfied with the antenatal care service. The type of health facility, education status, number and initiation time of antenatal visit, history of stillbirth, and waiting time to get service were factors associated with pregnant women’s satisfaction with antenatal care services.