Critical thinking is one of the most important elements in making the right decision in every profession. Evidence based practice shows potential to empower the critical thinking skills of practitioners. The aim of this study was to determine the effect of evidence-based information management and practice (EBIMP) training course on the promotion of medical librarians’ critical thinking. This study is a randomized double-blind educational trial in the form of a parallel trial. A sample of 60 librarians were recruited nationwide in the study through the volunteer enrollment to the evidence-based information management and practice training course. Intervention group received a 10-module virtual course focusing on evidence-based information management. But the control group received a basic course of evidence-based medicine. The courses were delivered through virtual learning system and data was collected through California Standard Critical Thinking Skills Questionnaire Form B (CCTST). Data were analyzed with Covariance Analysis (ANCOVA), Chi-square (χ²), Kolmogorov-Smirnov and Levin tests, and t-test, using SPSS 25. The findings showed that the critical thinking skills of participants after training of the information management and evidence-based practice (EBIMP) had significant improvement in the intervention group compared with the control group regarding the “inference” (4.86 ± 1.94 vs 4.20 ± 1.32), “assessment” (7.90 ± 1.77 vs 5.90 ± 1.70), “Inductive reasoning” (8.67 ± 2.32 vs 6.37 ± 1.87), “deductive reasoning” (6.47 ± 2.04 vs 5.77 ± 1.97) subskills. Education of evidence-based information practice could be effective in promotion of critical thinking skills of medical librarians. This study suggests evidence-based information practice to be added to the curriculum of medical library and information science fields. Trial registration: This study was registered with number 9000.1v1 in Registry of Efficacy and Effectiveness Studies (REES).