Long noncoding RNAs (lncRNAs) are >200 bp molecules that do not generally code for proteins. Human lncRNAs have well-characterised roles in gene expression regulation, particularly with regards to protein-coding genes, and their dysregulation has been linked to disease. Here, we set out to investigate changes in the expression of lncRNAs related to apoptosis and autophagy in the peripheral blood mononuclear cells (PBMCs) of rheumatoid arthritis (RA). Additionally, we aimed to correlate lncRNA expression profiles with clinical indexes and self-perception of patients (SPP). To this end, we employed RNA-sequencing of lncRNAs in PBMCs from three RA patients and three healthy controls. We used bioinformatics to screen several dysregulated lncRNAs related to apoptosis and autophagy. To validate key lncRNA candidates, we performed reverse transcriptase-quantitative polymerase chain reaction (qRT-PCR) on 20 RA patients and 20 healthy controls. We found the expression of seven lncRNAs (MAPKAPK5-AS1, ENST00000619282, C5orf17, LINC01189, LINC01006, DSCR9, and MIR22HG) was significantly altered in PBMCs of RA patients. Receiver operating characteristic (ROC) curve analysis suggested that MIR22HG (AUC = 0.846, p = 0.000), DSCR9 (AUC = 0.783, p = 0.005), LINC01189 (AUC = 0.677, p = 0.034), MAPKAPK5-AS1 (AUC = 0.644, p = 0.025) and ENST00000619282 (AUC = 0.636, p = 0.043) are potential biomarkers of RA. Spearman correlation analysis revealed selected lncRNAs correlated with clinical indexes and SPP. Therefore, we highlight some lncRNAs related to apoptosis and autophagy may serve as potential biomarkers for diagnosis and monitoring of RA progression, which also correlate with several clinical indexes and SPP. This article is protected by copyright. All rights reserved.