Background: The clinical decision support systems (CDSSs) for prescription medications is one of the technologies aimed at improving physician practice behavior and patient outcomes by reducing drug prescription errors. This study, thus, was conducted to investigate the effect of various CDSSs on physician practice behavior and patient outcomes.Methods: This systematic review was conducted by searching in PubMed, EMBASE, Web of Science, Scopus and Cochrane Library from 2005 to 2019. Two researchers independently evaluated the studies. Any discrepancies over the eligibility of the studies between the two researchers were then resolved by consulting a third researcher. Finally, we extracted data from the articles. Then, we conducted a meta-analysis based on medication subgroups and outcome categories; we also presented a narrative form of the findings. Meanwhile, we applied random-effects model to estimate the effects of CDSS on patient outcomes and physician practice performance with 95% confidence interval. Q statistics and I2 was then used to measure heterogeneity.Results: Based on the inclusion criteria, 46 studies were considered eligible for the analysis in this review. The CDSS for prescription medications had been used for various diseases such as cardiovascular diseases, hypertension, diabetes, gastrointestinal and respiratory diseases, AIDS, appendicitis, kidney disease, malaria, high blood potassium, and mental disease. Meanwhile, other cases such as the concurrent prescription of multiple drugs for patients and its effects on the above-mentioned outcomes were evaluated. The analysis shows that in some cases the application of CDSS provides positive effects on patient outcomes and physician practice behaviors. The effect was statistically significant (std diff in means =0.114, 95% CI: 0.090 to 0.138) as overall. It was also statistically significant for outcome groups such as those showing improved outcomes on physician practice performance and patient outcome or both. No significant difference was observed in comparison between some other cases and conventional methods. We think that this could be due to the disease type, the quantity, and the type of CDSS requirements that influenced the comparison. Conclusions: Our findings suggest that positive effects of the CDSS are due to factors such as user-friendliness, compliance with clinical guidelines, patient and doctor cooperation, integration of electronic health records, CDSS and pharmaceutical systems, consideration of the views of physicians in assessing the importance of CDSS alerts, and their real-time alerts in the prescription.