The damage caused by contusive traumatic brain injuries (TBIs) is thought to involve breakdown in neuronal communication through focal and diffuse axonal injury along with alterations to the neuronal chemical environment, which adversely affects neuronal networks beyond the injury epicenter(s). In the present study, functional connectivity along with brain tissue microstructure coupled with T2 relaxometry were assessed in two experimental TBI models in rat, controlled cortical impact (CCI) and lateral fluid percussive injury (LFPI). Rats were scanned on an 11.1 Tesla scanner on days 2 and 30 following either CCI or LFPI. Naive controls were scanned once and used as a baseline comparison for both TBI groups. Scanning included functional magnetic resonance imaging (fMRI), diffusion weighted images (DWI), and multi-echo T2 images. fMRI scans were analyzed for functional connectivity across laterally and medially located region of interests (ROIs) across the cortical mantle, hippocampus, and dorsal striatum. DWI scans were processed to generate maps of fractional anisotropy, mean, axial, and radial diffusivities (FA, MD, AD, RD). The analyses focused on cortical and white matter (WM) regions at or near the TBI epicenter. Our results indicate that rats exposed to CCI and LFPI had significantly increased contralateral intra-cortical connectivity at 2 days post-injury. This was observed across similar areas of the cortex in both groups. The increased contralateral connectivity was still observed by day 30 in CCI, but not LFPI rats. Although both CCI and LFPI had changes in WM and cortical FA and diffusivities, WM changes were most predominant in CCI and cortical changes in LFPI. Our results provide support for the use of multimodal MR imaging for different types of contusive and skull-penetrating injury.