Partnerships have become increasingly important in addressing complex global health challenges, a reality exemplified by the COVID-19 pandemic and previous infectious disease epidemics. Partnerships offer opportunities to create synergistic outcomes by capitalizing on complimentary skills, knowledge and resources. Despite the importance of understanding partnership functioning, research on collaboration is sparse and fragmented, with few conceptual frameworks applied to evaluate real-life partnerships in global health. In this study, we aimed to adapt and apply the Bergan Model of Collaborative Functioning (BMCF) to analyse partnership functioning in the UK Public Health Rapid Support Team (UK-PHRST), a government–academic partnership, dedicated to outbreak response and research in low- and middle-income countries. We conducted a literature review identifying important elements to adapt the framework, followed by a qualitative case study to characterize how each element, and the dynamics between them, influenced functioning in the UK-PHRST, exploring emerging themes to further refine the framework. Elements of the BMCF that our study reinforced as important included the partnership’s mission, partner resources (skills, expertise and networks), leadership, the external environment, management systems and communication. Additional elements identified in the literature and critical to partnership functioning of the UK-PHRST included governance and financial structures adopted, trust and power balance, organizational culture, strategy and evaluation and knowledge management. Because of the way the UK-PHRST was structured, fostering team cohesion was an important indicator of synergy, alongside collaborative advantage. Dividing the funding and governance equally between organizations was considered crucial for maintaining institutional balance; however, diverse organizational cultures, weak communication practices and perceived power imbalances compromised team cohesion. Our analysis allowed us to make recommendations to improve partnership functioning at a critical time in the evolution of the UK-PHRST. The analysis approach and framework presented here can be used to evaluate and strengthen the management of global health partnerships to realize synergy.