Cytoplasmic aggregation of transactive response DNA-binding protein 43 (TDP-43) is a hallmark of amyotrophic lateral sclerosis (ALS) and occurs in 57% of Alzheimer's disease (AD) cases. TDP-43 regulates RNA processing, including cryptic exon splicing. Here, we demonstrate that TDP-43 directly controls growth-associated protein (GAP43) expression by binding to its pre-mRNA. Loss or hyperphosphorylation of TDP-43 disrupts this binding, leading to the inclusion of cryptic exon 4a1, which introduces premature stop codons and reduces GAP43 protein levels. RNA sequencing analysis of ALS and AD brains revealed GAP43 downregulation, while 4a1 is upregulated in AD cases with phosphorylated TDP-43. TDP-43 knockdown impaired axonal regeneration in induced pluripotent stem cell (iPSC)-derived motor neurons, whereas GAP43 restoration rescued this defect. These findings suggest that the loss of GAP43 contributes to neurodegeneration in ALS and AD. The inclusion of GAP43 cryptic exon 4a1 may serve as a hallmark of TDP-43 proteinopathies, highlighting a mechanistic link between TDP-43 dysfunction and neuronal vulnerability.