Thrombocytopenia (TCP) is the second most common hematological change during pregnancy and is considered as a major source of maternal and neonatal morbidity and mortality. Despite its effects to morbidity and mortality, it is frequently ignored or disregarded, particularly in resource-limited nations. Thus, the purpose of this study was to determine the prevalence of thrombocytopenia and associated factors among pregnant women attending antenatal care at Hiwot Fana Comprehensive Specialized University Hospital, Eastern Ethiopia from June 20 to August 30, 2022. A hospital-based cross-sectional study was conducted among 199 pregnant women selected through a systematic sampling technique. Ethical approval was obtained from the Ethics Review Committee of Haramaya University. Data related to sociodemographic and reproductive variables were collected using structured questionnaires. Four milliliters of venous blood were collected from each study participant and a complete blood cell count was determined using UniCel DxH 800 hematology analyzer. Logistic regression analysis was done to assess the association between TCP and independent variables and P < .05 was considered statistically significant. In this study, the prevalence of TCP was 14.1% (95% CI: 9.6–19.7). Of them, 10 (35.7%), 12 (42.9%), and 4 (21.4%) had mild, moderate, and severe TCP, respectively. Having more than 3 children (adjusted odds ratio, AOR = 7.90, 95% CI: 2.60, 24.3), no antenatal care follow-up (AOR = 7.90, 95% CI: 2.40–26.2), being in the second and third trimester (AOR = 6.90, 95% CI: 1.70, 28.9 and AOR = 5.04, 95% CI: 1.12, 22.7, respectively), and history of heavy menstrual bleeding (AOR = 4.03, 95% CI: 1.25, 13.1) were significantly associated with TCP. TCP is a public health problem among pregnant women in the study area. Having more than 3 children, lack of antenatal care follow-up, being in the second and third trimesters, and having history of heavy menstrual bleeding was significantly associated with TCP. As a result, regular platelet count monitoring and appropriate intervention approaches based on identified predictors should be explored to mitigate adverse outcomes in pregnant women.