Partnerships between developed and developing country institutions are increasingly becoming important in addressing contemporary global health challenges faced by health systems. Inter-university health collaboration such as the Nottingham Trent University (UK) and Makerere University School of Public Health (Uganda) partnership provide opportunities for working together in training, research and service delivery while strengthening health systems. This paper shares the experiences, achievements and opportunities of this partnership in co-learning and supporting the health system in Uganda. This includes a project being implemented to strengthen the training, supervision and motivation of community health workers in rural Uganda. Training and research are a key focus of the partnership and have involved both staff and students of both institutions including guest lectures, seminars and conference presentations. The partnership’s collaboration with stakeholders such as the Ministry of Health (Uganda) and local health authorities has ensured participation necessary in supporting implementation of sustainable interventions. The partnership uses several channels such as email, telephone, Skype, Dropbox and WhatsApp which have been useful in maintaining constant and effective communication. The challenges faced by the partnership include lack of funding to support student mobility, and varying academic schedules of the two institutions. The experiences and prospects of this growing partnership can inform other collaborations in similar settings.