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Maternal syphilis caused substantial adverse pregnancy outcomes, even in women receiving antenatal care, including early fetal death, stillbirth, preterm birth, low birth weight, neonatal death, and congenital infection in infants. Though there are studies conducted on sero-prevalence of syphilis in Ethiopia, no recent studies were conducted in the West Guji zone. In spite of that, this study assessed the magnitude of syphilis and associated factors among pregnant mothers attending public health institutions in the West Guji zone, Oromia, Ethiopia. A facility based cross sectional study design was conducted in west Guji zone public health facilities from March 1 to April 30, 2024. A face-to-face interview was conducted. Finally, a systematic random sampling technique was applied to select 498 study participants. The data was entered into Epi-Data version 4.1 and exported to SPSS Statistics Version 27 for analysis. Descriptive analyses was computed to .summarize statistics and proportions. Multivariable logistic regression analysis was carried out by adjusted odds ratios and 95% confidence intervals. Statistical significance is declared at P < 0.05. Four hundred ninety-eight (498) pregnant women participated in the study, which yielded a 97% response rate. The prevalence of syphilis was 3% (95% CI: 1.2–4.8). Having a husband of no formal education [AOR = 7.2, 95% CI (1.3–43.9)], a history of abortion [AOR = 5.9, 95% CI (1.2–30.4)], multiple sexual partners [AOR = 7.4, 95% CI (1.4–39.4)], and alcohol use [AOR = 7.6, 95% CI (1.6–36.4)] were significantly associated with the prevalence of syphilis. Syphilis cases are prevalent in the study area. The statistically significant factors with syphilis were the educational status of the husband, history of abortion, multiple sexual partners, and alcohol use. Therefore, further efforts by policymakers, health institutions, and future researchers are important to tackle this disease by raising the awareness of the community towards secure sexual practice, the modes of transmission, and the awareness of the prevention of both infections and partner testing.