Subarachnoid hemorrhage (SAH) is an important cause of mortality in stroke patients. Long non-coding RNAs (LncRNAs) have important functions in brain disease, however their expression profiles in SAH remain to be elucidated. The present study aimed to investigate the expression signatures of LncRNAs and mRNAs in early brain injury (EBI) following SAH in a rat model. Male Wistar rats were randomly divided into an SAH group and a sham operation group. The expression signatures of the LncRNAs and mRNAs in the temporal lobe cortex were investigated using a rat LncRNAs array following experimental SAH. The results revealed that there were 144 downregulated and 64 upregulated LncRNAs and 181 downregulated and 221 upregulated mRNAs following SAH. Additionally, two upregulated (BC092207, MRuc008hvl) and three downregulated (XR_006756, MRAK038897, MRAK017168) LncRNAs were confirmed using reverse transcription quantitative polymerase chain reaction. The differentially expressed mRNAs were further analyzed using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The pathway analysis results provided by the KEGG database indicated that eight pathways associated with inflammation were involved in EBI following SAH. In conclusion, these results demonstrated that the expression profiles of the LncRNAs and mRNAs were significantly different between the SAH-induced EBI group and the sham operation group. These differently expressed LncRNAs may be important in EBI following SAH.