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Background: Bite jumping appliances (BJA) are a common treatment modality for Class II malocclusions and yet studies have shown that the results are limited to mostly dentoalveolar correction. A better understanding of the role the muscles of mastication play in the action of these appliances is warranted. Botulinum neurotoxin type A (BoNT/A) is a useful research tool to decrease muscle function without impeding blood supply or causing scarring. Objectives: BoNT/A was used in this study in combination with BJA to assess cephalometrically the effects that muscular stretch have on the skeletal outcomes of bite jumping therapy. Methods: One hundred and twenty-eight inbred, juvenile, male, Wistar Kyoto (WKY) rats were randomly assigned to either: one of six short-term groups, or one of ten long-term groups (n = 8 per group). The short-term groups consisted of C (control), S (saline injection), B (BoNT/A injection), M (BJA), MB (BoNT/A injections plus BJA), MS (saline injection plus BJA). The long-term groups consisted of CL (control), BL (BoNT/A injection), BLR (BoNT/A repeat injection), SL (saline injection), SLR (saline repeat injection), ML (BJA), MBL (BoNT/A plus BJA), MBLR (BoNT/A repeat injection plus BJA), MSL (saline injection plus BJA), and MSLR (saline repeat injection plus BJA). In the BoNT/A injection groups the temporalis and deep masseter muscles were injected bilaterally with Dysport®. Equivalent volumes of saline were used within the sham injection groups. In the repeat injection groups, the injections were repeated weekly for the duration of the study. Digital lateral and dorsoventral cephalometric radiographs were taken at baseline (T0 = 28 days old) and weekly thereafter for 3 weeks until T3 (49 days of age) at which time the short-term groups were culled and all appliances removed. Additional radiographs were taken in the long-term groups at T4 (56 days of age), T5 (70 days of age), T6 (98 days of age), and T7 (126 days of age). The cephalometric program Viewbox 3.1® was used to create cephalometric analyses and obtain linear and angular measurements. After an initial repeatability study the variables were restricted to those deemed more accurate. Multiple comparisons between and within groups were conducted using one-way ANOVA with post-hoc test Tamhane. Results: Importantly, the total mandibular length (Co↔Dg) and horizontal projection of the mandible were increased in the MBL and MBLR groups. The condyles also maintained a more anterior position in the MBL and MBLR groups. Conclusions: The length of the mandible was only slightly affected in the experimental groups. The mandibular condyle and glenoid fossa of the rat does possess some adaptive capacity to altered extrinsic forces.