Background: Scabies is a skin infection with global public health impact. Scabies is common in boarding schools due to overcrowding and limited hygiene. This study assesses the prevalence of scabies and related factors among students in a traditional Islamic boarding school in an urban area. Methods: This cross-sectional study was conducted in a traditional boarding school in South Jakarta, Special Capital Region of Jakarta, Indonesia. A total of 178 male students participated by completing a structured questionnaire and undergoing dermatological examinations for the diagnosis of scabies. The purpose of the questionnaire was to assess the knowledge and behavior of students. The data were analyzed using a chi-square test to evaluate associations between variables. Results: The study found that 43.8% of students were diagnosed with scabies, with highest number of cases occurring in students over 24 years old. Among scabies-positive students, 57.7% had moderate knowledge about scabies, and 47.4% practiced good preventive behavior. Most knowledge and hygiene-related factors, including skin, hand, and clothing hygiene, were not significantly associated with scabies prevalence. (p > 0.05). Bedding cleanliness was the only factor significantly associated with scabies (OR = 2.009, 95% CI 1.087–3.712, p = 0.037). Conclusion: The prevalence of scabies among students in a traditional urban Islamic boarding school in Indonesia was high. Students with poor bedding cleanliness had twice the risk of scabies compared to those with clean bedding. While many practiced positive hygiene behaviors, significant knowledge gaps about scabies persisted. Therefore, implementation of a school-level scabies control program that combines routine screening and prompt treatment with targeted hygiene interventions and education are suggested to bridge the knowledge-behavior gap. © The Author(s) 2025.