METHODS AND FINDINGS: This mixed method (qualitative and quantitative) study was conducted from 2018 to 2019 using a self-administered questionnaire among Muslim medical doctors from 2 main medical associations with a large number of Muslim members from all over Malaysia who attended their annual conference. For those doctors who did not attend the conference, the questionnaire was posted to them. Association A had 510 members, 64 male Muslim doctors and 333 female Muslim doctors. Association B only had Muslim doctors; 3,088 were female, and 1,323 were male. In total, 894 questionnaires were distributed either by hand or by post, and 366 completed questionnaires were received back. For the qualitative part of the study, a snowball sampling method was used, and 24 in-depth interviews were conducted using a semi-structured questionnaire, until data reached saturation. Quantitative data were analysed using SPSS version 18 (IBM, Armonk, NY). A chi-squared test and binary logistic regression were performed. The qualitative data were transcribed manually, organized, coded, and recoded using NVivo version 12. The clustered codes were elicited as common themes. Most of the respondents were women, had medical degrees from Malaysia, and had a postgraduate degree in Family Medicine. The median age was 42. Most were working with the Ministry of Health (MoH) Malaysia, and in a clinic located in an urban location. The prevalence of Muslim doctors practising FGC was 20.5% (95% CI 16.6-24.9). The main reason cited for practising FGC was religious obligation. Qualitative findings too showed that religion was a strong motivating factor for the practice and its continuation, besides culture and harm reduction. Although most Muslim doctors performed type IV FGC, there were a substantial number performing type I. Respondents who were women (adjusted odds ratio [aOR] 4.4, 95% CI 1.9-10.0. P ≤ 0.001), who owned a clinic (aOR 30.7, 95% CI 12.0-78.4. P ≤ 0.001) or jointly owned a clinic (aOR 7.61, 95% CI 3.2-18.1. P ≤ 0.001), who thought that FGC was legal in Malaysia (aOR 2.09, 95% CI 1.02-4.3. P = 0.04), and who were encouraged in religion (aOR 2.25, 95% CI 3.2-18.1. P = 0.036) and thought that FGC should continue (aOR 3.54, 95% CI 1.25-10.04. P = 0.017) were more likely to practice FGC. The main limitations of the study were the small sample size and low response rate.