Objective Cortical basal ganglionic degeneration (CBGD) is a rare neurodegenerative disease affecting the cortex and basal ganglia asymmetrically. The symptoms of the disease are generally resistant to therapy. In this report, we present the effects of repetitive transcranial magnetic stimulation (rTMS) on the decapacitating apraxia in two patients with CBGD. Methods Patient 1 is a 55 year-old man and Patient 2 is an 80 year-old woman. Apraxia was remarkably more prominent on the right side in both of them. 1 Hz and teta-burst stimulation was applied on the less affected motor cortex (M1) while 10 Hz stimulation was applied on the more affected M1. Responses to rTMS sessions were evaluated with nine-hole peg test (9-HPT), Purdue-Pegboard test and apraxia tests. Results Periods of recovery from apraxia were observed following certain rTMS sessions on the background of the natural progression of the disease. Conclusions Variable motor cortical excitability changes are seen in CBGD. Temporary recovery of the symptoms may be provided by rTMS modulation of the equilibrium of cortical excitabilities between the two hemispheres.