PurposeDrug use in prisons remains a public health concern because it is often the place of drug initiation. The purpose of this study was to analyze the drug use in prison in Burkina Faso.Design/methodology/approachWe conducted cross-sectional study in the prison of Ouagadougou. The adult prisoners (male and female) incarcerated for more than one month at the largest prison of Burkina Faso were included in the study. Participants were selected using a systematic random sampling. Data were collected from October 28 to November 26, 2018. The face-to-face interviews were conducted in the prison grounds. Logistic multivariate regression was used to identify factors associated with in prison drug use. All analysis was done using Stata.FindingsA total of 379 prisoners were included in this study. Approximately one-third inmates (32.71%; n = 124) experienced illicit drug in lifetime. Nearly one-third (28.76%; n = 109) of the prisoners were drug users before incarceration and 11.87% (n = 45) used drug inside the prison, of which 33.33% (n = 15) initiated drug use in the prison. Cannabis was the first drug used by the prisoners (71.11%) followed by tramadol (62.22%), diazepam (13.33%) and cocaine (2.22%). Four prisoners (3.63%) had reported Heroin use before incarceration. Cannabis was mainly smoked. Tramadol, diazepam and amphetamines were swallowed or mixed with food. Cocaine is smoked and snorted. Case of injection of cocaine and heroin was reported before incarceration. Main factors independently associated with drug use in prison is drug use before prison and young age of inmates. Indeed, inmates who had reported drug use before prison had 4.01 time {adjusted odd ratio (AOR: 4.01 [95% CI: 1.91–8.41])} higher odds to use drug in prison.Research limitations/implicationsTo conduct the interviews in the prison grounds could be a limitation due to social desirability bias. Indeed, the prisoners may understate drug use in prison for the fear of likely additional sentence. Availability of biological tests for drug markers might help addressed this bias. Nevertheless, the findings of this study should help to plan effective drug use prevention and care programs for prisoners.Practical implicationsThe actions must include the implementation of a medical and psychological care in continuum of healthcare system in Burkina Faso. This system should include screening at entry and adequate health and psychological care in prison for drug users for an effective control of drugs use in prison.Social implicationsMost of these drug users in prison have a low level of education and are unemployed. Education activities and training on occupational activities to prepare drug users for a successful social reintegration less dependent on drugs is essential. This study can be a basis to explore more possibilities and find out what is available to help those with substance use disorder, manage these cases in prison and prevent relapse on release.Originality/valueTo the best of the authors’ knowledge, this study is the first study on drug use in prison in Burkina Faso. It indicates that the repressive strategy against drug use seems ineffective because former users continue their consumption inside and also new users are initiated to use drugs in prison.