Abstract: In malaria endemic countries, national malaria control programs have been challenged to change treatment policy from time to time. Many of these countries have complex health care systems with the public and private sectors working alongside each other. Effective malaria treatment policy change and implementation demands appropriate response from both the public and private health sectors. We examined the changes in drug stocks, malaria prescription patterns and service utilization at public, private-not-for profit (mission) and private-for-profit health facilities in Uganda over a 36 month period of malaria policy change discussions and pronouncement. Time series analysis of manually extracted data from hospital patient records was used to determine the variations in attendance, drug availability and prescribing patterns. Key informant interviews were used to understand the perceptions of stakeholders about the effectiveness and implications of policy change. Public facilities were found to be more compliant to the national policy pronouncement. Differences in stock adjustments and prescription patterns were observed among the three facility types despite the adequate level of awareness about the policy change. Main reasons for non-compliance were unacceptable side effects, high cost of new regimen and poor treatment outcomes for the public, private-not-for profit and private-for-profit facilities, respectively.