In the United States, the phenomenon of mass incarceration has created a public health crisis. One strategy for addressing this crisis involves developing a correctional agency – academic institution partnership tasked with augmenting the quality and quantity of evidence-based healthcare delivered in state prisons and attracting a greater number of health professionals to the field of correctional health research. Using a Connecticut correctional agency – academic institution partnership as a case example, the present paper examines some of the key challenges encountered over the course of a 3-year capacity-building initiative. Particular attention is given to agency and institution characteristics both at the structural level and in terms of divergent stakeholder perspectives. The authors find that future partnership development work in this area will likely benefit from close attention to predictable sources of temporal variation in agency capability to advance project-related aims.