Purpose Scaphocephaly is the premature closure of the sagittal suture. The treatment strategies mainly focus on correcting the shape of the head, but there are very limited studies examining changes in brain structure. This study aimed to investigate shape differences in the shape of corpus callosum regarding the pre-treatment and post-treatment term at scaphocephaly patients. Methods Cranium shape data were collected from the two-dimensional digital images. The generalized Procrustes analysis was used to obtain mean shapes in the pre- and postoperative phases. The shape deformation of the corpus callosum from the pre- to postoperative phases was evaluated using the thin plate spline method. Results There is an enlargement of the splenium part of corpus callosum in the late group. In the early group, corpus callosum genu and body enlargement were observed in the postoperative period compared to the preoperative period, followed by a narrowing of the isthmus region. Conclusion This study showed structural deformations in the corpus callosum in scaphocephaly patients using head shape with the landmark-based geometric morphometric method by taking into consideration the topographic distribution. An enlargement at the splenium part of corpus callosum exposes after the cranial vault expansion depending on time.