Skeletal muscle atrophy occurs rapidly as a result of inactivity. Although there are many reports on changes in gene expression during the early phase of muscle atrophy, the patterns of up-and downregulated gene expression after long-term and equilibrated muscle atrophy are poorly understood. In this study, we comprehensively examined the changes in gene expression in long-term denervated mouse muscles using RNA-Seq. The murine right sciatic nerve was denervated, and the mice were housed for five weeks. The cross-sectional areas of the hind limb muscles were measured using an X-ray CT system 35 days after denervation. After 28 d of denervation, the cross-sectional area of the muscle decreased to approximately 65% of that of the intact left muscle and reached a plateau. Gene expression in the soleus and extensor digitorum longus (EDL) muscles on the 36th day was analyzed using RNA-Seq and validated using RT-qPCR. RNA-Seq analysis revealed that three genes—Adora1, E230016M11Rik, andGm10718—were upregulated and one gene—Gm20515—was downregulated in the soleus muscle; additionally, four genes—Adora1,E230016M11Rik,Pigh, andGm15557—were upregulated and one gene—Fzd7—was downregulated in the EDL muscle (FDR < 0.05). Among these genes,E230016M11Rik, one of the long non-coding RNAs, was significantly upregulated in both the muscles. These findings indicate thatE230016M11Rikcould be a candidate gene for the maintenance of atrophied skeletal muscle size and an atrophic state.