Abstract Background Substance use has a terrible impact on health, behavior and country’s economy because the number of people particularly the youngsters being involved in this practice is increasing rapidly. However, the prevalence, determinants and consequence of substance use in the study area has been overlooked. Methods A descriptive quantitative cross-sectional study was conducted among 254 health science students of Haramaya University. The respondents were selected randomly after double stratification based on their department and batch respectively. A pre-tested self–administrable anonymous questionnaire was used. The collected data were entered into epidata version 3.1 and exported to SPSS version 23. Descriptive statistical analysis was done to examine findings. Besides, chi-square (X²) test was considered to examine the nonparametric association of factors with ever substance use. Results Prevalence of ever substance use for at least one substance was found to be 114(45.4%). Ever khat chewers take the highest percentage [107(93.9%)] followed by ever smokers 45(39.5%) and ever drinkers 44(38.6%). Among these ever substance users, 80(70.2%) were found to be current substance users. Being a preparatory student (26.3%) and freshman at university (57.9%) were critical times to initiate substance use. Sex, monthly income, sexual risk behavior and family history of substance use were found to be significantly associated with being ever substance user as witnessed by their respective X² values of 19.67, 72.28, 28.99 and 139.72 at P-value = 0.05 and degree of freedom (d_f = 1). From the overall ever substance users, 31.6% had undesirable health consequences. Among these consequences, anorexia [40 (35.1%)] accounted for the highest percentage followed by insomnia [29 (25.4%)], depression [25 (22%)], gastritis [25 (22%)], dental caries [23 (20.2%)] and increased sexual activity [12 (10.5%)]. Conclusion Prevalence of ever substance use in the study area was relatively high. Therefore attention should be given to the major reasons for substance use mainly orientation of freshman students about better stress coping mechanisms and expansion of adequate recreational activities.