Significance Ebola virus (EBOV) infection is a severe, often fatal disease with poorly understood pathophysiology. Here, we performed [ ¹⁸ F]-DPA-714 Positron Emission Tomography (PET) in a macaque model of EBOV infection to longitudinally track and quantify the translocator protein (TSPO), an immune cell marker. The imaging findings, along with immunohistology and other disease markers, showed increasing stem cell proliferation in the bone marrow, along with progressive monocytic and lymphocytic loss in the spleen and lungs. This study provides real-time noninvasive assessment of EBOV pathogenesis and disease progression, as well as the associated host responses, at the organ level. This approach can be similarly used to study other inflammatory and infectious diseases and to test the efficacy of newly developed therapeutics and vaccines.