The purpose of this study was to examine the challenges facing managers in managing conflict in schools of South and South Central Regions of Botswana. In this study, the schedule of interview was used to collect empirical data. A random sample of 50 school managers and deputy school managers was selected for interviews. Major findings of the study revealed that school managers do not perceive conflict as an inevitable phenomenon that is real in any organization. They lack skills and strategies of handling conflict positively to produce good results. The study recommended that school managers should be trained on the importance and benefits of conflict. This training in conflict management will give them a skill that can enable them to turn conflict erupting in their schools into a positive force that can bring a positive change.