Rabies is endemic in southern Bhutan and children were reported to be the most frequent victims. We surveyed the knowledge, attitude, and practices on rabies among school children in three schools located in southern Bhutan. Descriptive statistics and logistic regression were performed to analyze the level of knowledge and variation of perception towards rabies among secondary school children. A total of 701 students (57.9% female, 42.1% male) had participated in the survey of which 98.2% heard about rabies. Most of the students demonstrated a good level of knowledge (59.7%) and a favorable perception towards rabies (57.7%). Multivariable logistic regression analysis revealed the importance of previous rabies awareness campaign increasing the likelihood of positive knowledge about rabies at the individual student and the school level. Similarly, higher grades of students’, employed mothers of the students, and students from villages were associated with more favorable perceptions. Overall, our study in rabies endemic areas of Southern Bhutan showed that most of the students have good knowledge and favorable perception towards rabies. However, we identified several knowledge gaps. Therefore, efforts should be made to address the knowledge gaps through regular awareness programs by actively engaging key stakeholders such as school-teachers and parents.