The purpose of this study is to evaluate whether the effects of botulinum neurotoxin (botox) injection into the masseter in the mandibular condylar cartilage (MCC) and subchondral bone could be rescued by compressive loading of the temporomandibular joint (TMJ). Twenty-four 6-week-old female mice (C57BL/6J) were used. Mice were divided in three groups: (1) Botox (n = 8); (2) Botox plus loading (n = 8); (3) Pure control (n = 8). Bone labels (3 and 1 day before sacrifice) and the proliferation marker EdU (2 and 1 day before sacrifice) were intraperitoneally injected into all groups of mice. Condyles were dissected and examined by micro-CT and histology. Sagittal sections of condyles were stained for TRAP, alkaline phosphatase, EdU, TUNEL, and toluidine blue. In addition, immunostaining for pSmad, VEGF, and Runx2 was performed. Bone volume fraction, tissue density, and trabecular thickness were significantly decreased on the subchondral bone of botox-injected side when compared to control side and control mice, 4 weeks after injection. Furthermore, histological analysis revealed decrease in mineralization, matrix deposition, TRAP activity, EdU, and TUNEL-positive cells in the MCC of the botox-injected side, 4 weeks after injection. However, compressive loading reversed the reduced bone volume and density and the cellular changes in the MCC caused by Botox injection. TMJ compressive loading rescues the negative effects of botox injection into the masseter in the MCC and subchondral bone.