In this paper, the authors identify the critical areas for systems strengthening to improve alternative care for young children in Uganda. Using evidence, the paper sheds light on the current status of child vulnerability which necessitates alternative care, examines the situation of alternative care, and underlines the growing reliance on institutionalization of children as a first line of response, instead of using it as a last resort. The chapter presents the collaborative involvement of the government, Makerere University and civil society organizations as one of the promising practices aimed at strengthening the child protection system with focus placed on the practice-oriented, tailor-made training programs targeting in service workers to handle child protection issues. Other areas that need particular attention to build an effective government-led child protection system are identified including increased funding, legislation, building functional management information systems, coordination and leadership, and improving data collection and research.