Background: Healthcare is a basic human right extending across all humanitarian contexts, including conflict. Globally, two billion people are living under conditions of insecurity and violent armed conflict with a consequent impact on public health. Health research in conflict-affected regions has been recognised as important to gain more understanding of the actual needs of such populations, to optimise healthcare delivery, as well as to inform advocacy and policy change. International collaborative research maximises the resources and skills available for dealing with global health issues, builds capacity and endeavours to ensure the research reflects real needs of the populations. Under the UK’s Global Challenge Research Fund in 2017 a number of such international programs were created including the Research for Health in Conflict-Middle East and North Africa (R4HC-MENA) partnership to build capacity in conflict and health research as well as study specific areas, namely noncommunicable diseases in conflict (cancer & mental health) and the political economy of health in conflict. Methods: A qualitative study using semi-structured online interviews was conducted to explore researchers’ and stakeholders’ perspectives on the R4HC-MENA programme over its lifetime from 2017 to 2021. It aimed to understand the factors that influenced and accelerated international collaboration within the R4HC-MENA programme on conflict and health research, and to provide deeper insights into the implementation of the programme. Data collection was conducted from March 2022 to June 2022. Purposive and snowball sampling techniques were used for participant recruitment. Thematic analysis was applied for data analysis. Results: Twelve researchers/stakeholders participated in this study: four men and eight women. Four main themes were generated: Theme 1: Network building (personal and institutional levels); Theme 2: Hierarchies and power dynamics (power imbalance between different academic status, genders and institutions); Theme 3: Communication challenges; Theme 4: Career development (management, leadership, research, and teaching skills). Conclusions: This study provided preliminary insights into perspectives on international collaboration in a major international programme of research on conflict and health. Several key challenges and outputs were generated by the researchers in this study. The findings are important for further developing effective strategies to tackle the challenge of power imbalance and ineffective communication in international research collaborations.