Objective: To perform an in silico bioinformatics analysis to identify differentially expressed microRNAs (miRNAs) implicated in rheumatoid arthritis (RA) pathogenesis and evaluate their potential as biomarkers for assessing therapeutic efficacy and monitoring acupuncture treatment. Methods: miRNA microarray data (CEL and TXT formats) were acquired from human and murine RA models, with the latter undergoing acupuncture treatment. Data were normalized using the robust multi-array average (RMA) method and analyzed for differential expression. Differential expression analysis identified miRNAs through a comparative analysis of RA human tissues, acupuncture-treated murine RA models, and a bibliographic search for miRNAs implicated in RA pathogenesis and acupuncture treatment. Bioinformatics analysis was performed to identify potential target genes for each miRNA and signaling pathways via search tools for the Retrieval of Interacting Genes/Proteins (STRING) and ShinyGO. Gene-drug interaction analysis was performed through Drug-Gene Interaction Database (DGIdb) screening. Interaction networks were constructed with the Cytoscape v3.10.3 software. Results: The hsa-miR-125a-5p and hsa-miR-125b-5p were identified as potential biomarkers associated with RA pathogenesis, presenting 468 and 455 target genes, respectively. These genes were enriched in 20 signaling pathways, including Janus kinasa-signal transducer and activator of transcription (JAK-STAT), mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase-protein kinase B (PI3K-Akt), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway, which have been associated with RA pathogenesis and progression. Drug-gene interaction networks revealed that 22 genes were significantly associated with 58 RA treatment drugs, among which 13 genes interacted with members of the hsa-miR-125 family. Conclusion The hsa-miR-125a-5p and hsa-miR-125b-5p demonstrate critical regulatory role in RA pathogenesis by modulating signaling pathways, including JAK-STAT, MAPK, PI3K-Akt, and NF-κB. Our findings show that the hsa-miR-125a-5p and hsa-miR-125b-5p exhibit differential expression patterns in response to pharmacological intervention in various diseases, including RA management. This suggests their potential roles as biomarkers for monitoring acupuncture treatment. Although existing evidence indicates that acupuncture can modify miRNA expression profiles, rigorous validation through biological models remains essential to confirm these results.