Despite recent advances in diagnostic and therapeutic modalities for infectious and autoimmune encephalitis, the management of patients with suspected or confirmed encephalitis poses a great challenge to physicians. Neuroimaging, including magnetic resonance imaging (MRI) and positron emission tomography (PET) scanning, can play a crucial role in substantiating the diagnosis of encephalitis and eliminating clinical mimics of encephalitis from consideration. Moreover, characteristic neuroimaging patterns can aid in defining specific infectious and autoimmune etiologies. Volumetric and functional MRI, in particular, are being increasingly used to characterize outcomes following encephalitis and can shed light on brain reorganization and function after the acute phase of disease has resolved. Here, we discuss the uses of structural, functional, and PET neuroimaging in the clinical assessment of the acute and recovery phases of encephalitis.