Based upon an ethnography of two biomedical, scientific research institutes in Uganda funded primarily by donors in the Global North, this article examines the political economy of knowledge production in global health science. Specifically, I use the concept of precarity to illustrate the ways in which funding instabilities for scientific research shape the making of knowledge. I do this at three levels: the macro level of funding institutions, the meso level of research institutes, and the micro level of individual projects. Through analysing the experiences of researchers in these institutional environments, I elucidate the ways in which the political economy of global health science—particularly short-term, grant funding—constrains and enables knowledge production. I thus argue that for many scientists the priority of renewing or obtaining funding supersedes that of conducting research that is closely tied to local issues. Whilst I do not contend that the latter is unimportant to scientists, this article highlights the existential precarities fomented by the possibility of not being funded and argues that they play a substantial role in influencing the foci of global health science research projects, thus alienating them from the needs and interests of the people they are intended to benefit.