Inflammation may play a role in the development of epilepsy after brain insults. [C-11]-(R)-PK11195 binds to TSPO, expressed by activated microglia. We quantified [C-11]-(R)-PK11195 binding during epileptogenesis after pilocarpine-induced status epilepticus (SE), a model of temporal lobe epilepsy. Nine male rats were studied thrice (D0-1, D0+6, D0+35, D0=SE induction). In the same session, 7T T2-weighted images and DTI for mean diffusivity (MD) and fractional anisotropy (FA) maps were acquired, followed by dynamic PET/CT. On D0+35, femoral arterial blood was sampled for rat-specific metabolite-corrected arterial plasma input functions (AIFs). In multiple MR-derived ROIs, we assessed four kinetic models (two with AIFs; two using a reference region), standard uptake values (SUVs), and a model with a mean AIF. All models showed large (up to two-fold) and significant TSPO binding increases in regions expected to be affected, and comparatively little change in the brainstem, at D0+6. Some individuals showed increases at D0+35. AIF models yielded more consistent increases at D0+6. FA values were decreased at D0+6 and had recovered by D0+35. MD was increased at D0+6 and more so at D0+35. [C-11]-(R)-PK11195 PET binding and MR biomarker changes could be detected with only nine rats, highlighting the potential of longitudinal imaging studies.