In 2018 only 35.8% of schools in Indonesia had implemented PHBS, and in 2019 only 22.5% of schools in Aceh had implemented Clean and Healthy Behaviors. This study aims to compare the implementation of PHBS in santri of modern pesantren with traditional Islamic boarding schools in Aceh. This study uses a quantitative method with a comparative study and a total sampling method with 368 students. The data collection tool used was the standard PHBS questionnaire—data analysis using Mann Whitney test and multiple linear regression. The results of this study indicate that there are differences in knowledge (p-value = 0.613), attitudes (p-value = 0.377), PHBS (p-value = 0.094), basic sanitation, have received counseling when to get counseling. There is a difference in action (p-value = 0.000) for santri of modern pesantren with traditional pesantren in Aceh. Knowledge, attitudes, and actions affect PHBS behavior, which means that there is no most dominant factor affecting the PHBS of santri in modern and traditional Islamic boarding schools.