Canonical and non-canonical Wnt signaling pathways are well-characterized regulators of retinal development. Wnt signaling also promotes neuroprotection and regeneration in adult tissues, including retinal ganglion cell (RGC) survival and axonal regrowth after optic nerve injury. However, it is unknown whether Wnt-dependent neuroprotection after injury in the adult CNS is associated with altered expression of developmental genes. Muller glia are a prominent radial glia type in the retina that play critical roles in retinal neuron protection, RGC neurite growth, and axon regeneration by acting through Wnt and other signaling pathways. We recently used mass spectrometry to characterize proteins secreted from Muller glia in response to Wnt signaling. In this study, we investigated whether the Wnt-induced Muller glia secretome includes proteins involved in development and whether their corresponding genes are regulated by Wnt5a during axonal regeneration in a mouse model of optic nerve crush (ONC) injury. Adult mice received intravitreal injections of Wnt5a or saline at the time of ONC injury, and then retina tissue was collected at early time points post-injury. The expression of candidate Wnt-regulated developmental genes and related proteins were characterized by qPCR and immunohistochemistry. Our findings revealed that Wnt5a downregulated the expression of specific developmental genes, including cilia-related genes Nphp4, INTU, and Jade1, as well as transcriptional regulators Pax6 and Tsc1, with time-dependent changes observed during axonal regrowth. Several of these genes were localized to RGCs and inner nuclear layer cells, suggesting direct effects in RGCs and contributions from Muller glia. These results demonstrate that specific developmental gene pathways are suppressed by Wnt5a in association with RGC survival and axon regrowth following injury. Therefore, this study adds to our knowledge of potential mechanisms of Wnt-mediated optic nerve regeneration and identifies new categories of putative regeneration-regulating genes for further study.