Syphilis is a chronic infectious disease caused by the spirochaete Treponema pallidum. It has significant long-term morbidity for mothers and can cause serious complications in pregnancy, which may result in spontaneous abortion, stillbirth and other negative outcomes including congenital syphilis. There is currently, no data on the burden of syphilis in pregnant women in Juba Southern Sudan. A cross-sectional study was carried out in three antenatal clinics in Juba information collected was on demographics (level of education, marital status, occupation history of abortion and others). About 231 consenting pregnant women were recruited using a standard questionnaire and 5ml of blood was collected. Samples were tested for syphilis using both RPR and TPHA tests. Out of the 231 samples 51 (22.1%) tested positive for active syphilis. Significant risk factors identified were being a housewife, history of abortion and history of partner travel, while attending antenatal clinic for previous pregnancy was associated with having less syphilis factor. Factors which were not significantly associated with syphilis were polygamous marriages (p= 0.355), given birth before (p= 0.386) and duration of stay with partner (p= 0.161). The prevalence of syphilis in pregnant women in Juba Southern Sudan is still high compared to other studies. Results show that screening and treating mothers for syphilis in their first visit to ANC can reduce the prevalence and outcomes of syphilis in pregnancy. Syphilis routine testing in ANC and pregnant women should be encouraged to attend ANCs.