The role of the Heads of Departments (HoDs) in the school structure is to provide middle leadership. They assist the principals on the day to day leadership of the schools. They are responsible for ensuring the achievement of their departmental and school vision and mission. This study sought to explore the nature of the challenges faced by the HoDs in the Lesotho context. The study was framed within the interpretive paradigm and adopted a qualitative approach. The participants consisted of sixteen HoDs and eight school principals. These participants were purposively selected and then interviewed through the focus groups and semi-structured interviews. The findings revealed that the HoDs face several challenges that hinder their performance. For example, they lack the requisite skills to perform their duties. They also encounter considerable resistance from their peers. In the light of the findings, we argue that it is crucial for the HoDs to be afforded the empowerment and support that they need so that they can do their job efficiently. This support may benefit their schools as well as the entire education sector.