Background Substance Use Disorder is a chronic relapsing disease that is characterized by compulsive drug seeking and use, despite harmful consequences. The aim of this study was to evaluate the impact of clinical pharmacist intervention/recommendation on the treatment of patients admitted to addiction rehabilitation centers in Jordan. Methods A randomized controlled trial was conducted in two public addiction treatment centers in Amman. Patients (n = 93) were randomized into 2 groups (control and intervention). Medication review was conducted for both groups at baseline, during stay and at discharge. Treatment related problems (TRPs) were identified by the clinical pharmacist and recommendations provided to the therapeutic team in the intervention group. Additionally, quality of life and quality of sleep were assessed at baseline and 2 weeks later. Results A total of 392 TRPs were identified during the study period. The mean number of TRPs ± SD was 4.22 ± 2.58 per patient. The clinical pharmacist intervention led to a reduction in the mean number of TRPs at discharge by 2.2 ± 0.85 (p < 0.001) in comparison to the control group (by 0.23 ± 0.27, p = 0.066). After 2 weeks of admission, there was an improvement of physical health (p = 0.035) and of the overall sleep status (p = 0.048) in the intervention vs. control groups. Conclusion Clinical pharmacy services provided to patients with substance use disorder reduced the number of TRPs and improved other outcomes such as physical health and quality of sleep during detoxification. Long term studies with larger sample sizes are needed.