Ependymoma (EPN) is a type of tumor that occurs in the central nervous system of children and adults. EPN produces resistance to chemotherapy, and there are no targeted drugs available as a proper cure. Therefore, the use of high-throughput sequencing technologies to elucidate pathogenic mechanisms is of prime importance to identify potential tumor target genes helpful for developing effective therapeutic approaches against EPN. With this objective, we used RNA-seq analysis to identify differentially expressed genes (DEGs) and pathways in 4 pairs of EPN tissues and adjacent tissues. In total, we found 5,445 differentially expressed genes. The synaptic vesicle cycle and extracellular matrix (ECM) receptor interaction pathways were highly enriched in the ependymoma group. Nine differentially expressed genes (SNAP25, GRM4, CELSR1, LAMA1, WNT5A, ROR2, CCND1, EPHB2, FOXJ1) were randomly verified by RT-qPCR, supporting the authenticity of our sequencing results. This study provides global gene information and some new potential biomarkers for the diagnosis and therapeutic targets of ependymoma.