SCIRR39 is an identified upregulated gene in rat primary neuron injury and/or regeneration process with roles largely unexplored. Using real-time quantitative PCR, Western blotting and immunofluorescence, SCIRR39 expression was detected in normal PC12 cells and upregulated in differentiated cells. The results of cell proliferation by Cell Counting Kit and cell cycle by flow cytometry indicated that SCIRR39 inhibited cell proliferation and induced the decrease in S phase. Importantly, immunofluorescent and RhoA pull-down assays showed that SCIRR39 strongly affected the neurite extension of NGF-treated PC12 cells through a RhoA-dependent mechanism, but the truncated mutants of SCIRR39 containing a truncation from 141AA to 211AA or from 397AA to 424AA failed to mock the SCIRR39 effect on neurite extension. Moreover, change of SCIRR39 expression in NGF-treated PC12 cells regulated the expression and phosphorylation of Fyn, a regulator of RhoA activity, but not the expression of ROCK II protein. Finally, immunofluorescence and RhoA pull-down assays revealed that obvious inhibition of neurite extension by SCIRR39 shRNA was reversed by RhoA inhibitor C3-transferase. Our results indicated that SCIRR39 increased the neurite extension in NGF-treated PC12 cells via RhoA, suggesting that SCIRR39 contributes to the regeneration of neuron injury by specifically altering the differentiation program.