Background. Thrombocytopenia is the second most common hematological disorder in pregnancy after anemia worldwide and affects 7-8% of all pregnancies. Pregnant women with thrombocytopenia have complications of excessive bleeding during or after childbirth, exudation at the cesarean section, and neonatal thrombocytopenia. Therefore, the main aim of this study was to assess the magnitude of thrombocytopenia and its associated factors among pregnant women attending the Antenatal Care Service Unit of Wachemo University Nigist Ellen Mohammed Comprehensive Specialized Hospital Hosanna, Southern Ethiopia. Materials and Methods. A cross-sectional study was conducted from June 1 to August 30, 2022, involving 209 consecutive pregnant women who came to the hospital during the study period for antenatal care follow-up. Sociodemographic, reproductive, and other clinical data were collected using a structured questionnaire. A four-milliliter venous blood specimen was collected for complete blood analysis and peripheral blood smear. The data were analyzed by using SPSS version 25. Descriptive statistical analysis and bivariate and multivariate logistic regression analyses were performed. A P value ≤0.05 was considered to indicate statistical significance. Results. The overall magnitude of thrombocytopenia among pregnant women was 14.8% (95% CI: 10, 19.6). The prevalence of mild, moderate, and severe thrombocytopenia was 77.4%, 16.1%, and 6.5%, respectively. Multivariate logistic regression revealed that rural residence (AOR = 2.6 and 95% CI = 1.02, 7.12), cigarette smoking (AOR = 8.4 and 95% CI = 1.86, 38), anemia (AOR = 8.3 and 95% CI = 2.7, 25.6), and alcohol consumption (AOR = 8.2 and 95% CI = 2.17–31) were significantly independent factors associated with the development of thrombocytopenia. Conclusion. The magnitude of thrombocytopenia in this study was 14.8%. Rural residence, cigarette smoking, alcohol consumption, and anemia were significantly associated with thrombocytopenia. Therefore, the platelet count should be routinely determined during antenatal care visits for proper diagnosis and to minimize bleeding during and/or after childbirth.