The corpus callosum is the major brain structure responsible for the transferring of information between the two hemispheres. In congenital agenesis of the corpus callosum (ACC), an alternative functional connection might exist between the hemispheres; however, this has yet to be demonstrated. The present study evaluated a 27-year-old man with ACC but no detectable motor function deficits using diffusion tensor imaging (DTI), movement-related cortical potential (MRCP), and interhemispheric inhibition (IHI). The MRCP was analyzed at the electrodes of C3, FCZ, and C4. IHI was measured using paired transcranial magnetic stimulation over the hand area of the primary motor cortex at both hemispheres. Data of the patient were compared with those of an age-matched healthy control group (n = 8, mean age: 27.6 ± 2.5 years). DTI showed absence of the callosal fibers and the presence of enhanced transcommissural fibers in the ACC patient. The mean fractional anisotropy of the transcommissural fibers revealed a significant difference between the patient and the control group (0.62 vs. 0.43, p < 0.01). The MRCP and IHI, supposed to be highly relevant to the transcallosal pathway, were present in the patient though they occurred to a relatively low degree compared to the control group. Findings suggest that in the ACC patient, the abnormal transcommissural fibers might be functional and serve as an alternative pathway connecting the bilateral hemispheres.