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),