Recent studies have demonstrated that the BRAF(V600E) mutation is associated with aggressive clinicopathological features of papillary thyroid carcinoma (PTC). However, the BRAF mutation as a prognostic biomarker in papillary thyroid microcarcinoma (PTMC) is unclear. A systematic search of the electronic databases, including Medline, Scopus, CNKI and the Cochrane Library was performed up to July 1, 2014. Outcomes of interest included age, gender, concomitant hashimoto thyroiditis or nodular goiter, tumor size, pathological stage, tall cell variant of PTMC (TCVPTMC), multifocality, extrathyroidal extension (ETE) and lymph node metastasis (LNM). A total of 19 studies published from 2008 to 2014 comprising 2253 patients fulfilled the inclusion criteria and were included in the meta-analysis, and 1143 (50.7%) of these patients were BRAF mutation positive. BRAF mutation was associated with larger tumor size (OR: 1.64; 95% CI: 1.16-2.32), multifocality (OR: 1.58; 95% CI: 1.25-2.00), ETE (OR: 2.59; 95% CI: 2.03-3.29), LNM (OR: 1.73; 95% CI: 1.14-2.62), advanced stage (OR: 2.03; 95% CI: 1.14-3.64) and TCVPTMC (OR: 5.07; 95% CI: 1.49-17.27; P=0.009). Additionally, the BRAF mutation was found to be not associated with age, gender, concomitant hashimoto thyroiditis or nodular goiter (P>0.05 for all). This meta-analysis revealed that in patients with PTMC, BRAF mutation is associated with tumor size, multifocality, ETE, LNM, advanced stage and TCVPTMC, and it may be used as a predictive factor for prognosis of PTMC.