To make sustainable progress towards universal health coverage (UHC), public health financing is very critical. Uganda has taken major budgetary reforms to optimize budget planning, transparency, and accountability since the early 2000s. The two major reforms over this period include the shift from an input-based budget approach to output-oriented budgeting (OOB) in FY 2008/09, followed by the introduction of Programme Based Budgeting (PBB) in FY 2017/2018. The PBB has been shown to improve allocation efficiency through better expenditure prioritization and ensuring that resources get to where they are needed and on time. This has the potential to ensure adequate and equal access to quality healthcare services and financial protection for the vulnerable population. This document provides the results of an assessment that reviews the status of PBB implementation in the health sector, to inform and strengthen the transition to PBB and thus improve health service delivery outcomes. The report describes the transition from OOB to PBB and provides an analysis of the current budget structure. Some of the suggestions from this assessment have been key in ensuring that the full potential of the PBB reform is realized in Uganda. For example, the urgent need to improve the interconnectivity of the Performance Budgeting System (PBS) tool with other Public Financial Management (PFM) tools such as the Financial Management Information System, the Integrated Personnel and Payroll System, and the Debt Management System.