This study investigates rhythmic jaw movement (RJM) patterns and masticatory muscle activities during electrical stimulation in two cortical masticatory areas in obese male Zucker rats (OZRs), compared to their counterparts—lean male Zucker rats (LZRs) (seven each). At the age of 10 weeks, electromyographic (EMG) activity of the right anterior digastric muscle (RAD) and masseter muscles, and RJMs were recorded during repetitive intracortical micro-stimulation in the left anterior and posterior parts of the cortical masticatory area (A-area and P-area, respectively). Only P-area-elicited RJMs, which showed a more lateral shift and slower jaw-opening pattern than A-area-elicited RJMs, were affected by obesity. During P-area stimulation, the jaw-opening duration was significantly shorter (p< 0.01) in OZRs (24.3 ms) than LZRs (27.9 ms), the jaw-opening speed was significantly faster (p< 0.05) in OZRs (67.5 mm/s) than LZRs (50.8 mm/s), and the RAD EMG duration was significantly shorter (p< 0.01) in OZRs (5.2 ms) than LZR (6.9 ms). The two groups had no significant difference in the EMG peak-to-peak amplitude and EMG frequency parameters. This study shows that obesity affects the coordinated movement of masticatory components during cortical stimulation. While other factors may be involved, functional change in digastric muscle is partly involved in the mechanism.