Significance The cerebral cortex is the most highly evolved structure in the human brain. Generating the correct number and types of neurons is crucial for brain function. We show a central role of the Lhx2 homeoprotein in this task: deleting Lhx2 in cortical progenitors leads to a temporal shift of neurogenesis initiation, resulting in a much smaller cortex with decreased numbers of neurons in all cortical layers. Further, we found that Lhx2 is required for the Wnt/β-catenin pathway to maintain progenitor proliferation. Using a parsimonious mathematical model, we demonstrated that such disruptions of neurogenesis timing are enough to explain the cortical size and thickness modifications observed. Our findings enlighten how neurogenesis timing is regulated molecularly and how it affects cortical size and organization.