Background Hepatitis B virus infection is considered a serious health problem in developing countries since it causes chronic liver cirrhosis, hepatocellular carcinoma, and hepatic failure. The risk of acquiring HBV is four times higher in HCWs compared to non-HCWs. Medical students are also considered a high-risk group for HBV infection for their exposure to body fluids and blood during medical training in health facilities. The purpose of this study is to evaluate HBV vaccination coverage and associated factors among medical students in Bosaso universities, Somalia. Methodology: An institutional-based cross-sectional study has been conducted in four universities. The online raosoft sample size calculator has been used to calculate the sample size. A stratified sampling method is employed to draw participants from the four universities. In each university, the research participants were selected using a simple random sampling technique. Self-administered questionnaires have been distributed among 247 medical students. Data were analyzed by using the SPSS version 21, and findings were presented in tables, and proportions. Results Only 2.8% were fully vaccinated, while 5.3% have ever started taking the HBV doses. The main reasons for not getting vaccinated against Hep B included unavailability of the vaccines (32.8%), high vaccine cost (26.7%), fear of vaccine side effects (12.6%), lack of trust in vaccine quality (8.5%,), lack of awareness of the vaccine whereabouts (5.7%), and lack of time (2.8%). Occupation, monthly income, marital status, and availability of testing policy in the workplace were associated with HBV vaccine uptake with a correlation coefficient of 0.3, 0.2, 0.13, and 0.2, respectively (P-value < 0.05). 73.7% of the respondents scored higher than the average knowledge score regarding knowledge of HBV. Conclusion The vaccination coverage among medical students in Bosaso was very low (2.8%) and sheds light on the urgent importance of a National HBV infection elimination policy to be developed with Hep B vaccines being available and easily accessible to those at high risk including medical students. Expansion of the sample size to include multiple cities for increased representativeness plus Hepatitis B titer tests is recommended.