For the last two decades Uganda embraced many political, economic and policy reforms to revamp her collapsed economy. One of these has been decentralisation as is enshrined in her 1995 National Constitution and the 1997 LGA. Decentralisation in the healthcare sector was specifically adopted to improve management efficiency and effectiveness, increase local representation and community responsibility, to strengthen financial performance through increased revenue generation and rational expenditure decisions, facilitate the provision of public goods and services more efficiently among others. Through a decentralised healthcare system, many actors have entered into the healthcare delivery businesses with a number of service provision mechanisms, interests and expectations. This has benefited the healthcare sector. However, many problems that existed in the centrally-controlled healthcare system have either re-surfaced or been exacerbated, despite deliberate efforts to tackle them. That led to the emergence of various challenges, which call for serious attention, if the gains made are not to be eroded and render Ugandan unable to attain its health-related MDG targets by 2015.