Introduction: Scabies has been a continuous health concern in residential institutions including boarding schools in Indonesia. The disease easily spreads in overcrowding residences. Using one of several boarding schools in Medan, Indonesia, as study site, we conducted this study to better understand the underlying factors behind scabies incidence in boarding schools. We hoped to be able to promote more effective preventive measures toward the disease. Materials and Methods: We included all of 220 students (115 males and 105 females) in a cross-sectional descriptive analytical study, whose ages were ranging from 10 to 18 years. The diagnosis of scabies was made based on interview and physical examination. Skin scraping followed by microscopic assessment was carried out upon finding scabies-related lesion. Data on risk factors were collected using a set of pretested questionnaire and direct observation. Data were analyzed using bivariate and multivariate analysis the with Chi square and logistic regression. Results: We found a high prevalence clinical scabies, i.e., 81 (36.8%) students, yet only one came out positive with skin scraping and microscopic examination. The factors associated with the infection were found to be younger age (odds ratio [OR]: 2.95, 95% confidence interval [CI] 0.97–6.09), sharing clothes (OR: 8.22, 95% CI 2.37–28.48), sharing bed (OR: 17.53, 95% CI 5.55–56.02), and unhygienic bedroom condition (OR: 8.18, 95% CI 3.30–20.28). Conclusions: The results imply the need for better strategies to prevent the transmission of astigmatid mites within the risky populations. We promote six recommendations for a more applicable approach toward scabies prevention in boarding schools and other institutional facilities alike.