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Introduction: Adequate and sustainable funding of national medicine regulatory agencies (NMRAs) is key for assurance of quality, safety and efficacy of medical products circulating in a market. The study aimed to determine factors affecting NMRAs funding in five East African Community (EAC) countries namely: Burundi, Kenya, Rwanda, Tanzania (Mainland and Zanzibar) and Uganda., Methodology: An exploratory, mixed method design using both qualitative and quantitative data, was employed. Data from six NMRAs was collected through a combination of semi-structured interviews, questionnaires, and checklists for the period 2011/12-2014/15 while 2010/11 data served as baseline. Interviews were conducted with heads of NMRAs and monitoring and evaluation experts of the respective agencies. NMRA's financing was assessed using six indicators namely, funding policy, financial autonomy, the total annual budget, actual funding per annum, funds received from various sources, and the NMRA expenditure., Results: The average total annual budget for all the EAC countries during the study period 2011-2015 ranged from USD 824,328.67 to USD 10,724,536.50. The low budget in Zanzibar may be attributed to population and pharmaceutical market size. Uganda's attainment of 98.75% (USD 10,656,704) revenue from industry fees is a result of deliberate government policy change from 100% reliance on donor funding over a period of 10 years (1995-2015). On average, the proportion of revenue against budget per annum is 54.8% (USD 458,970.11), 98.7% (USD 10,302,295.25) and 100% (USD 7,375,802.08) for Zanzibar Food & Drugs Agency (ZFDA), Uganda National Drug Authority (NDA) and Tanzania Medicines and Medical Devices Authority (TMDA) respectively. Governments, industry fees and donors are the major sources of funding across all NMRAs in the EAC region, with TMDA and Uganda NDA relying more on industry fees by 73.20% (USD 4,664,777.59) and 98.25% (USD 8,077,238.20) respectively. While Burundi relies solely on government funding, ZFDA, on the other hand, received on average 50.40% (USD 252,557.22) from government and 40.60% (USD 165,303.34) from industry fees and the remaining 9% from donors and other sources. An overall contribution of funds received from donors by each NMRA was the least among other sources of financing. Observation of expenditure patterns indicated operational costs to be the major expense in the majority of the NMRAs, followed by salaries and infrastructure development. The Kenya NMRA has the highest degree of average expenditure across all three categories, with the least average expenditures being marked by Burundi NMRA. The operational costs on average increased considerably in all the NMRAs during the study period., Conclusion: Evidence from the EAC suggests that government and industry fees are the main sources of funding while donor contributions vary from country to country. Government policy, legal framework, and fees structure are the key enablers of NMRAs funding sustainability., Competing Interests: The authors have declared that no competing interests exist.