Background: Growing evidence has indicated that long non-coding RNAs (lncRNAs) are important regulators of pathological and physiological processes through various mechanisms. However, the signature of lncRNA expression and the possible roles of lncRNAs in spinal cord injury (SCI) rat neurogenic bladder (NB) have not been comprehensively explored. In this study, the expression profiles of lncRNAs and mRNAs were explored in the bladder tissue of SCI rats using next-generation sequencing (NGS). Methods: Twenty female Wistar rats were randomly divided into SCI 1-3 and normal control (NC) groups. The spinal cord was completely transected at the T9-T10 level to establish the SCI model. Bladder tissues were collected on days 7, 14, and 28 after the operation. The expression profiles of lncRNAs were detected by NGS. Differentially expressed lncRNAs (DELs) were chosen for qRT-PCR verification to validate the RNA sequencing results. The functions of the predicted target genes were then evaluated using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Results: Compared with the NC group, the SCI 1-3 groups had 468, 117, and 408 DELs [fold change (FC) >2], including 247, 38, and 201 up-regulated and 163, 79, and 207 down-regulated lncRNAs, respectively. Likewise, 6,654, 2,133, and 5,706 mRNAs (FC >2) were differentially expressed between SCI 1-3 and NC rats, of which 4,821, 1,195, and 3,695 were up-regulated, and 1,833, 938, and 2,011 were down-regulated, respectively. Specifically, Miat, Mir155hg, and H19 were significant DELs in all SCI groups. Moreover, GO revealed that the DELs were related to several terms, including immune response, and KEGG was mainly enriched in 10 pathways, such as the transforming growth factor beta signaling pathway. Conclusions: The results revealed the expression profiles and possible roles of lncRNAs in SCI rat NB. This study may help identify possible NB mechanisms following SCI from the perspective of lncRNAs and provides new potential lncRNAs for the early diagnosis and treatment of human NB in the future.