In humanitarian contexts, it is a difficult and multi-faceted task to enlist academics, humanitarian actors and health authorities in a collaborative research effort. The lack of research in such settings has been widely described in the past decade, but few have analysed the challenges in building strong and balanced research partnerships. The major issues include considering operational priorities, ethical imperatives and power differentials. This paper analyses in two steps a collaborative empirical endeavour to assess health service utilization by Syrian refugee and Lebanese women undertaken by the International Committee of the Red Cross (ICRC), the Lebanese Ministry of Public Health (MoPH) and the Harvard François-Xavier Bagnoud (FXB) Center. First, based on challenges documented in the literature, we shed light on how we negotiated appropriate research questions, methodologies, bias analyses, resource availability, population specificities, security, logistics, funding, ethical issues and organizational cultures throughout the partnership. Second, we describe how the negotiations required each partner to go outside their comfort zones. For the academics, the drivers to engage included the intellectual value of the collaboration, the readiness of the operational partners to conduct an empirical investigation and the possibility that such work might lead to a better understanding in public health terms of how the response met population needs. For actors responding to the humanitarian crisis (the ICRC and the MOPH), participating in a technical collaboration permitted methodological issues to be worked through in the context of deliberations within the wider epistemic community. We find that when they collaborate, academics, humanitarian actors and health authorities deploy their respective complementarities to build a more comprehensive approach. Barriers such as the lack of uptake of research results or weak links to the existing literature were overcome by giving space to define research questions and develop a longer-term collaboration involving individual and institutional learning. There is the need ahead of time to create balanced decision-making mechanisms, allow for relative financial autonomy, and define organizational responsibilities. Ultimately, mutual respect, trust and the recognition of each other's expertise formed the basis of an initiative that served to better understand populations affected by conflict and meet their needs.