Background: Monk healers provide an accessible and popular service in Southeast Asia, but little is known on the substance use status of their clients. This investigation intended to assess and compare the rate and correlates of substance use disorders in two different treatment settings (monk healers=MH and primary health care=PHC) in Thailand. Methods: In a cross-sectional study, 1024 patients (591 of MH and 613 of PHC) responded to screening measures of the “World Health Organization Alcohol, Smoking, and Substance Involvement Screening Test Lite”, and two common mental disorders (major depression and generalized anxiety disorder) from November 2018 to February 2019. Logistic regression was used to estimate the determinants of any substance use disorder in the MH and PHC setting. Results: The prevalence of substance use disorder was higher in MH clients than PHC patients: any substance use disorder 11.7% (95% Confidence Interval-CI: 9.3%-14.5%) vs 5.4% (95% CI: 3.9%-7.5%), tobacco use disorder 7.6% (95% CI: 5.7%-9.9%) vs 2.5% (95% CI: 1.5%-4.0%), alcohol use disorder 10.0% (95% CI: 8.4%-13.6%) vs 4.3% (95% CI: 3.0%-6.3%), any drug use disorder 4.2% (95% CI: 2.8%-6.1%) vs 0.3% (95% CI: 0.08%-1.3%), and any past three months drug use 8.2% (95% CI: 6.2%-10.7%) vs 1.5%, 95% CI: 0.8%-2.8%). In adjusted logistic regression analysis, among MH clients, male sex (Adjusted Odds Ratio-AOR: 9.52, 95% Confidence Interval-CI: 5.06-17.92) was positively, and were married (AOR: 0.32, 95% CI: 0.16-0.61) and high social support (AOR: 0.40, 95% CI: 0.16-0.99) were negatively associated with any substance use disorder. Among PHC patients, male sex (AOR: 7.05, 95% CI: 2.99-16.63) was positively and age (AOR: 0.95, 95% CI: 0.92-0.98) was negatively associated with any substance use disorder. Conclusion: The proportion of substance use disorders among MH attendees was more than twice that of PHC attenders in Thailand, calling for collaboration in controlling substance use disorders between the two treatment systems.