This study of a global health research partnership assesses how U.S. fiscal administrative policies impact capacity building at foreign partner institutions. We conducted a case study of a research collaboration between Mbarara University of Science and Technology (MUST) in Mbarara, Uganda, and originally the University of California San Francisco (UCSF), but now Massachusetts General Hospital (MGH). Our case study is based on three of the authors' experiences directing and working with this partnership from its inception in 2003 through 2015. The collaboration established an independent Ugandan non-profit to act as a local fiscal agent and grants administrator and to assure compliance with the Ugandan labour and tax law. This structure, combined with low indirect cost reimbursements from U.S. federal grants, failed to strengthen institutional capacity at MUST. In response to problems with this model, the collaboration established a contracts and grants office at MUST. This office has built administrative capacity at MUST but has also generated new risks and expenses for MGH. We argue that U.S. fiscal administrative practices may drain rather than build capacity at African universities by underfunding the administrative costs of global health research, circumventing host country institutions, and externalising legal and financial risks associated with international work.