Progressive vaccinia (PV) is a rare but potentially lethal complication which develops in smallpox vaccine recipients with severely impaired cellular immunity. We report a patient with PV requiring treatment with vaccinia immune globulin and who received two investigational agents, ST-246 and CMX001. We describe the various molecular, pharmacokinetic, and immunologic studies which provided guidance to escalate and then successfully discontinue therapy. Despite development of resistance to ST-246 during treatment, the patient had resolution of his PV. This case demonstrates the need for continued development of novel anti-orthopoxvirus pharmaceuticals and the importance of both intensive and timely clinical and laboratory support in management of PV.