MicroRNAs (miRNAs/miRs) are small non-coding RNAs identified in plants, animals and certain viruses; they function in RNA silencing and post-transcriptional regulation of gene expression. miRNAs also serve an important role in the pathogenesis, diagnosis and treatment of tumors. However, few studies have investigated the role of miRNAs in thyroid tumors. In the present study, the expression of miRNA and mRNA was compared between follicular thyroid carcinoma (FTC) and follicular thyroid adenoma (FA) samples, and then miRNA-mRNA regulatory network analysis was performed. Microarray datasets (GSE29315 and GSE62054) were downloaded from the Gene Expression Omnibus, and profiling data were processed with R software. Differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) were determined, and Gene Ontology enrichment analysis was subsequently performed for DEGs using the Database for Annotation, Visualization and Integrated Discovery. The target genes of the DEMs were identified with miRWalk, miRecords and TarMir databases. Network analysis of the DEMs and DEMs-targeted DEGs was performed using Cytoscape software. In GSE62054, 23 downregulated and 9 upregulated miRNAs were identified. In GSE29315, 42 downregulated and 44 upregulated mRNAs were identified. A total of 36 miRNA-gene pairs were also identified. Network analysis indicated a co-regulatory association between miR-296-5p, miR-10a, miR-139-5p, miR-452, miR-493, miR-7, miR-137, miR-144, miR-145 and corresponding targeted mRNAs, including TNF receptor superfamily member 11b, benzodiazepine receptor (peripheral) -associated protein 1, and transforming growth factor β receptor 2. These results suggest that miRNA-mRNAs networks serve an important role in the pathogenesis, diagnosis and treatment of FTC and FA.