Previous studies have suggested high Immunodeficiency Virus (HIV) and hepatitis B virus (HBV) prevalence in prisons in Ghana. However, this study was part of a nationally representative bio-behavioural survey and determined the prevalence of HIV and HBV among prison inmates and identified factors associated with these infections. Both biomedical and behavioural data were collected from a total of 2,443 prison inmates from 19 prison stations during 2013 in Ghana; 12 male prisons and 7 female prisons selected across the country. The national HIV screening algorithm was used for HIV testing while two rapid detection tests were used to confirm HBV infections. HIV and HBV prevalence among prisoners in Ghana were approximately 2.34% and 12.38% respectively. Only 5 inmates, had co-infection with both viruses. The prevalence of HIV was significantly lower among male inmates (1.5%) compared to the female inmates (11.8%). Age, sex, and marital status, were significantly associated with both HIV and HBV infections. However, BMI category, IDU, and time spent in prison were associated with HIV infections. The educational level was significantly associated with HBV infections. After binary logistic regression, being female (AOR: 0.18, 95% CI: 0.07–0.45, p<0.001) and having a stay of 5 years or more (AOR: 0.07, 95% CI: 0.01–0.60, p = 0.016), increased the risk of having HIV infection. While, those with no formal education (AOR: 0.65, 95% CI: 0.45–0.95, p = 0.024) and are underweight (AOR: 0.51, 95% CI: 0.27–0.99, p = 0.046), were more likely to have HBV infection. Forced penetrative sex may be a problem in the prisons. The need to have and strengthen an integrated screening, treatment and vaccination plan for the prison is emphasized. The prison does not serve as an exceptionally high risk to the general population. The findings support a critical look at the issue of forced penetrative sex in the prisons.