The spread of HIV/AIDS is a major public health problem in military personnel in Africa. However, the epidemiological evidence regarding HIV/AIDS prevention practices among military personnel in Ethiopia remains unclear. The aim of this study was to investigate HIV/AIDS prevention practices among military personnel in Northwest Ethiopia. A cross-sectional study among military personnel (n = 410) was conducted in Northwest Ethiopia in 2015. Data were collected using a pre-tested questionnaire. Multivariable logistic regression model was fitted to ascertain factors influencing participation in HIV/AIDS prevention programs. About one-fourth (24.6%) of the military personnel had multiple sexual partners, of whom 24.7% failed to use condoms regularly when having sex with non-regular sexual partners. Majority of the sample (n = 355, 86.6%) participated in HIV/AIDS prevention programs. Military personnel who had multiple sexual partners were 6.3 times more likely to report history of non-participation in HIV/AIDS prevention programs (AOR = 6.3, CI95 = 3.5-11.54). A considerable proportion of military personnel had multiple sexual partners with lower levels of condom utilization with non-regular sexual partners. The study further demonstrated misconceptions about HIV/AIDS in Ethiopian military personnel, which reduce their likelihood of participation in HIV/AIDS prevention programs. Health authorities need to strengthen and accelerate HIV/AIDS prevention programs focusing towards military personnel.