Damage to the adult central nervous system often leads to severe motor and sensory deficits due to the inability of axons to regenerate after injury. Glial scar forms surrounding the injury site and acts as a barrier to prevent axon regrowth. Chondroitin sulfate proteoglycans (CSPGs) are known to be a component of the glial scar, playing a key role to inhibit axonal regeneration. Growing evidences reveal that receptor protein tyrosine phosphatase sigma (RPTPσ) is a main receptor for CSPGs and that CSPGs activate downstream small GTPase RhoA, however, the molecular link between RPTPσ and RhoA, still remained unclear. Here we report the identification of NME1/2, nucleoside diphosphate kinase, as a new direct downstream signaling molecule of RPTPσ that inhibits neurite outgrowth via upregulation of RhoA signaling. Using HEK293 cell lines transiently transfected with HA-tagged RPTPσ, we isolated the proteins that associated with RPTPσ by using affinity purification. Analysis of the complex by mass spectrometry identified NME1/2 as a potential RPTPσ binding partner. Role of NME1/2 in cancer cells has been well documented as inhibitor of small GTPase families, but its role in nervous system has not been understood yet. Therefore, we first confirmed NME1/2 protein expression in cortical neurons by immunohistochemestry. Then we performed knockdown of NME1/2 by transfection of shRNA vectors in cortical neurons and observed inhibition of neurite outgrowth as CSPGs treatment. NME1/2 overexpression rescues neurite outgrowth inhibition by CSPGs in cortical neurons. NME1/2 knockdown also alters small GTPase RhoA activity. From these results, we concluded that CSPG binds RPTPσ and upregulates the interaction with RPTPσ and NME1/2 followed by RhoA activation. Blockade of RPTPσ/NME1/2 signaling might enhance regeneration of CNS axons.