Background; Hepatitis B virus (HBV) is the world’s most common and highly contagious liver infection. Its transmission methods are: mother to child, via open wounds, sexual contact, blood transfusion and other blood contact related activities. Prevalence of HBV among pregnant women in Africa ranges from 3.67 - 16.5% and in Ethiopia 2.4 to 8.4%. Hepatitis B infection leads to high morbidity and mortality for mother as well as for their infants due to the vertical transmission. Hence assessing the prevalence and associated factors of Hepatitis B Virus infection is a priority. Methodology : An institution based cross sectional study was conducted with a total of 194 of pregnant women attending antenatal care at Agena health center from May 1-30/2019. Frequency analysis and Logistic regression test was used to determine the associated factors associated with Hepatitis B virus by using SPSS version 25. Results: The prevalence of HBV in Agena health center among pregnant women were 4.1% and it was associated with marital status, history of hospital admission and history of abortion. Conclusion : The prevalence of HBV in Agena health center among pregnant women was intermediate. Since routine screening and immunization of all pregnant women is mandatory. Key words : Hepatitis B infection, pregnant women, Agena health center