Mechanical loading is integral to bone development and repair. The application of mechanical loads through rehabilitation are regularly prescribed as a clinical aide following severe bone injuries. However, current rehabilitation regimens typically involve long periods of non-loading and rely on subjective patient feedback, leading to muscle atrophy and soft tissue fibrosis. While many pre-clinical studies have focused on unloading, ambulatory loading, or direct mechanical compression, rehabilitation intensity and its impact on the local strain environment and subsequent bone healing have largely not been investigated. This study combines implantable strain sensors and subject-specific finite element models in a pre-clinical rodent model with a defect size on the cusp of critically-sized. Animals were enrolled in either high or low intensity rehabilitation one week post injury to investigate how rehabilitation intensity affects the local mechanical environment and subsequent functional bone regeneration. The high intensity rehabilitation animals were given free access to running wheels with resistance, which increased local strains within the regenerative niche by an average of 44% compared to the low intensity (no-resistance) group. Finite element modeling demonstrated that resistance rehabilitation significantly increased compressive strain by a factor of 2.0 at week 1 and 4.45 after 4 weeks of rehabilitation. The resistance rehabilitation group had significantly increased regenerated bone volume and higher bone bridging rates than its sedentary counterpart (bone volume: 22.00 mm3 ± 4.26 resistance rehabilitation vs 8.00 mm3 ± 2.27 sedentary; bridging rates: 90% resistance rehabilitation vs 50% sedentary). In addition, animals that underwent resistance running had femurs with improved mechanical properties compared to those left in sedentary conditions, with failure torque and torsional stiffness values matching their contralateral, intact femurs (stiffness: 0.036 Nm/deg ± 0.006 resistance rehabilitation vs 0.008 Nm/deg ± 0.006 sedentary). Running on a wheel with no resistance rehabilitation also increased bridging rates (100% no resistance rehabilitation vs 50% sedentary). Analysis of bone volume and von Frey suggest no-resistance rehabilitation may improve bone regeneration and hindlimb functionality. These results demonstrate the potential for early resistance rehabilitation as a rehabilitation regimen to improve bone regeneration and functional recovery.