A significant limitation of the traditional randomized controlled trials is that strong preferences for (or against) one treatment may influence outcomes and/or willingness to receive treatment. Several trial designs incorporating patient preference have been introduced to examine the effect of treatment preference separately from the effects of individual interventions. In the current study, we summarized results from studies using doubly randomized preference trial (DRPT) or fully randomized preference trial (FRPT) designs and examined the effect of treatment preference on clinical outcomes. The current systematic review and meta-analysis was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies using DRPT or FRPT design were identified using electronic databases, including PubMed, Cochrane Library, EMBASE, and Google Scholar between January 1989 and November 2018. All studies included in this meta-analysis were examined to determine the extent to which giving patients their preferred treatment option influenced clinical outcomes. The following data were extracted from included studies: study characteristics, sample size, study duration, follow-up, patient characteristics, and clinical outcomes. We further appraised risk of bias for the included studies using the Cochrane Collaboration's risk of bias tool. The search identified 374 potentially relevant articles, of which 27 clinical trials utilized a DRPT or FRPT design and were included in the final analysis. Overall, patients who were allocated to their preferred treatment intervention were more likely to achieve better clinical outcomes [effect size (ES) = 0.18, 95% confidence interval (CI) 0.10-0.26]. Subgroup analysis also found that mental health as well as pain and functional disorders moderated the preference effect (ES = 0.23, 95% CI 0.11-0.36, and ES = 0.09, 95% CI 0.03-0.15, respectively). Matching patients to preferred interventions has previously been shown to promote outcomes such as satisfaction and treatment adherence. Our analysis of current evidence showed that allowing patients to choose their preferred treatment resulted in better clinical outcomes in mental health and pain than giving them a treatment that is not preferred. These results underline the importance of incorporating patient preference when making treatment decisions.