Significance The corpus callosum connects left and right cerebral cortices, integrating sensory-motor and associative functions, and is the largest connection in the human brain. While all mammals have a cerebral cortex, only eutherians evolved a corpus callosum. However, how this occurred remains largely unknown. We compared transcription factors that control subcerebral versus callosal neuron projection fates in eutherians and marsupials and found remarkably high similarity of their gene sequences and functions. However, expression of the callosal gene SATB2 was delayed in mice relative to dunnarts, and premature overexpression was sufficient for reversion to an ancestral-like brain phenotype. Our results suggest that transcriptional heterochrony might have influenced callosal evolution, and that complex traits can originate by differential deployment of existing regulatory genes.