BACKGROUND: In the last decade, Makerere University College of Health Sciences (MakCHS) has taken strides in research and training to improve healthcare through collaborative training and research programs. However, there is limited data on the trends of MakCHS faculty contributions to research and on faculty growth to take leading roles in health research. This paper reviews MakCHS faculty research publications over 15.5 years and outlines possible strategies to enhance faculty research outputs. METHODS: We used a mixed methods approach. A systematic review of research publications by faculty at MakCHS (PubMed and Google Scholar from January 1, 2000, to June 30, 2015) to quantify the number of research articles, areas researched, authorship contribution by MakCHS faculty, source of funding, as well as affiliated local and international collaborations. Graphs were used to shown trends in publications and leadership of authorship by faculty. Annual individual faculty research productivity was presented as publication per capita. Qualitative data on high priority needs to improve research outputs was collected through focus group discussions (FGDs) with faculty members, and analysed manually into emerging themes. RESULTS: Of 298 faculty at MakCHS at 2015, 89 (30%) were female and 229 (77%) were junior and mid-level faculty (senior lecturer and below). The PubMed and Google Scholar searches yielded 6927 published articles, of which 3399 (49%) full-text articles were downloaded for analysis, 426/3825 (11%) available as titles/abstracts only, and 598/4423 (14%) were excluded. Only 614 articles were published in 2014, giving a publication per capita of 2.1 for any authorship, and 0.3 for first and last authorship positions. MakCHS faculty increasingly contributed as first, second, third, and last authors. Up to 57% of research was in infectious diseases, followed by non-communicable diseases (20%) and non-communicable maternal child health (11%). Priority needs to improve research outputs, as expressed by faculty, were (1) an institutionally led faculty career development program, (2) skills building in research methods and scientific writing, (3) protected time for research related activities, (4) opportunities for collaborative research, and (5) use of individual development plans. CONCLUSION: Faculty research productivity was low and dominated by infectious diseases and non-communicable disease research. There is a need for structured institutional support to optimise faculty research outputs. Only with increased research productivity will MakCHS and other academic institutions be able to make a significant contribution in addressing national health challenges.