Many studies have suggested that microRNAs (miRNAs) might serve as novel diagnostic indicators of thyroid cancer (TC). However, inconsistent results have also been reported. This meta-analysis was conducted to assess the diagnostic value of miRNAs in discriminating malignant thyroid nodules from benign ones on fine-needle aspiration samples. A systematic literature search for relevant literature published up to April 5, 2014 was conducted in PubMed, Embase, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biological Medicine (CBM) databases. Data from different studies were pooled to estimate the summary sensitivity (SEN), specificity (SPE), positive likelihood ratios (PLR), negative likelihood ratios (NLR), diagnostic odds ratio (DOR), using the random-effect model. Summary receiver operator characteristic curves (SROCs) were plotted and areas under the SROC curve (AUC) were calculated to evaluate the overall test performance. Between-study heterogeneity was tested using the Q tests and the I (2) statistics. Potential sources of heterogeneity were analyzed through subgroup analyses and meta-regression. Deeks' funnel plot asymmetry test was performed to evaluate publication bias. All analyses were performed using STATA 12.0 software. Eighteen studies from 7 articles, including 543 patients with malignant thyroid nodules (n = 266) and benign ones (n = 277), were included in this meta-analysis. The pooled SEN was 0.77 (95 % CI: 0.70-0.83), SPN was 0.75 (95 % CI: 0.68-0.81), PLR was 3.1 (95 % CI: 2.4-4.0), NLR was 0.30 (95 % CI: 0.23-0.39), DOR was 10 (95 % CI: 7-16), and AUC was 0.83 (95 %CI: 0.79-0.86). Subgroup analyses indicated that multiple miRNAs assays showed a higher diagnostic accuracy than single miRNA assays. In conclusion, this meta-analysis suggests that miRNAs analysis can significantly improve diagnostic accuracy for differentiating malignant thyroid nodules from benign indeterminate ones on fine-needle aspiration (FNA) samples. With further confirmation, multiple miRNAs assays may play a critical role as a complement to fine-needle aspiration biopsy (FNAB).