A number of resolutions of the World Health Assembly and the WHO Regional Committee for Africa call upon African countries and their development partners to make the required investments in national health research systems (NHRS) to generate knowledge and promote its use in tackling priority public health challenges. Implementation of these resolutions is critical for Africa to progress with the rest of the world in achieving the post-2015 health sustainable development goal. This study assesses the current status of some NHRS components in the 47 countries of the WHO African Region, identifies the factors that enable and constrain NHRS, and proposes the way forward.To track progress in NHRS components and for comparison, a questionnaire that was used in NHRS surveys in 2003 and 2009 was administered in all 47 countries in the African Region. The national health research focal persons were responsible for completing the questionnaire, which had been hand-delivered to them by the WHO country office staff in charge of research, who also briefed them on the survey, went through the questionnaire for clarity, and sought their informed consent. All the 47 countries responded to the questionnaire, but some did not answer all questions. Of the countries responding to various questions 49 % (23/47) had a national health research policy; 47 % (22/47) had a health strategic plan; 40 % (19/47) had legislation governing research; 53 % (25/47) had a national health research priority agenda; 51 % (24/47) reported having a functional NHRS and a national health research management forum; 91 % (43/47) had anethical review committee; 49 % (23/47) had hospitals with ethical review committees to review clinical research proposals;51 % (24/47) had a scientific review committee; 62 % (29/47) had health institutions with scientific review committees; 83 % (39/47) had a national health research focal point; 51 % (24/47) had a health research programme; 55 % (26/47) had a national health or medical research institute or council; 93 % (41/44) had at least one university faculty of health sciences that conducted health research; and 33 % (15/46) had a knowledge translation platform. Forty-seven percent of countries reported having a budget line for research for health in the ministry of health budget. Between 2003 and 2014, the countries with a functional NHRS increased from 30 % to 51 %.Compared with 2003 and 2009 surveys, our survey found many countries to have made progress in strengthening some of the functions of their NHRS. However, there remains an urgent need for countries without NHRS to establish them and for others to improve the functionality and efficiency of every NHRS component. This is necessary for the national governments to effectively execute their leadership and governance of NHRS and to create an enabling environment within which research for health can flourish.