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Background  Despite being disproportionately burdened by preventable diseases than more advanced countries, low- and middle-income countries (LMICs) continue to trail behind other parts of the world in the number, quality and impact of scholarly activities by their health researchers. Our strategy at the Nigerian Implementation Science Alliance (NISA) is to utilise innovative platforms that catalyse collaboration, enhance communication between different stakeholders, and promote the uptake of evidence-based interventions in improving healthcare delivery. This article reports on findings from a structured group exercise conducted at the 2016 NISA Conference to identify (1) gaps in developing research capacity and (2) potential strategies to address these gaps.    Methods  A 1-hour structured group exercise was conducted with 15 groups of 2–9 individuals ( n  = 94) to brainstorm gaps for implementation, strategies to address gaps and to rank their top 3 in each category. Qualitative thematic analysis was used. First, duplicate responses were merged and analyses identified emerging themes. Each of the gaps and strategies identified were categorised as falling into the purview of policy-makers, researchers, implementing partners or multiple groups.    Results  Participating stakeholders identified 98 gaps and 91 strategies related to increasing research capacity in Nigeria. A total of 45 gaps and an equal number of strategies were ranked; 39 gaps and 43 strategies were then analysed, from which 8 recurring themes emerged for gaps (lack of sufficient funding, poor research focus in education, inadequate mentorship and training, inadequate research infrastructure, lack of collaboration between researchers, research-policy dissonance, lack of motivation for research, lack of leadership buy-in for research) and 7 themes emerged for strategies (increased funding for research, improved research education, improved mentorship and training, improved infrastructure for research, increased collaboration between academic/research institutions, greater engagement between researchers and policy-makers, greater leadership buy-in for research).    Conclusions  The gaps and strategies identified in this study represent pathways judged to be important in increasing research and implementation science capacity in Nigeria. The inclusion of perspectives and involvement of stakeholders who play different roles in policy, research and implementation activities makes these findings comprehensive, relevant and actionable, not only in Nigeria but in other similar LMICs.    Electronic supplementary material  The online version of this article (10.1186/s12961-018-0289-x) contains supplementary material, which is available to authorized users.

Gaps and strategies in developing health research capacity: experience from the Nigeria Implementation Science Alliance