We investigated the effect of the soluble Nogo66 receptor (sNgR-Fc) on the protection of cortical axons after cortical infarction in rats. The cortical infarction was induced by photothrombotic cortical injury (PCI) in Sprague-Dawley rats, after which sNgR-Fc was injected into the lateral ventricle. The ipsilesional cortices were harvested for analyses using histochemical and transmission-electron microscope techniques. The involved signaling pathways, which include RhoA, JNK, c-JUN and ATF-2, were detected by Western blot. Serious pathologies were found in the brains of the rats after injury, including edemas in the axoplasms of axons that have no medulla sheath and a thickening or shrinkage in the sheath of the axons that have medulla sheathes. However, these pathologies improved after sNgR-Fc treatment. The levels of GTP-RhoA, p-JNK, p-c-JUN and p-ATF-2 in the PCI group were increased when compared with their levels in the sham-operation group (P < 0.05), and animals receiving the sNgR-Fc treatment showed lower expression levels of these proteins when compared with the sham-operation group (P < 0.05). Our results suggest that sNgR-Fc can alleviate the pathological changes of axons following cortical infarction via decreasing the activation of RhoA/JNK signaling pathways.