Objectives To describe individual, interpersonal, and environmental factors and sexual risk behaviors among Thai Muslim adolescents. Methods We recruited adolescents from four schools and one vocational college on the Southern border of Thailand during October 2018 to January 2019. We used password-protected online questionnaires for each respondent to protect their privacy. Results We recruited N = 700 participants of which 9% were sexually experienced. Of those participants, many had never used a condom (41.3%) or considered taking contraceptive pills (71.4%). Moreover, 54% of them have had sexual intercourse more than once. Some had been infected with an STI (17.5%), and (14.3%) became pregnant more than once. Adolescents reported individual factors such as high religiosity (58.7%), and (47.6%) practiced Islam daily with no differences between boys and girls. Girls had significantly higher refusal of sex self-efficiency than boys (96 vs. 119.5, p < 0.05). In the interpersonal factors, boys had more uninvolved parenting style, lower parental monitoring, higher parental approval of sex, and higher perceived peer norm than girls. The environmental factors besides cultural norms impacted girls and boys equally. Conclusions We showed low rates of sexual activity, but in those adolescents who were sexually active we showed high rates of lack of knowledge and higher rates of sexual risk behaviors. Individual, interpersonal, and environmental factors all influenced sexual risk behaviors. We recommend comprehensive sexuality education that includes Islamic context for adolescents and their parents embedded in policy, religious, and community cultural practices.