The BRAF (V600E) mutation is a common genetic alteration in papillary thyroid carcinoma (PTC) and is associated with some pathological features. The association has been widely reported, but results were inconclusive. In this study a meta-analysis was done to explore the association between BRAF(V600E) mutation and pathological features in papillary thyroid carcinoma. Medline, PubMed and Web of Science were searched. A total of 69 studies that included 14,170 PTC patients were identified. The outcomes were from 2004 to October 2013. STATA12.0 software package was used to analyze the data. The result was assessed based on pooled odds ratios (ORs) with 95 % confidence intervals (CIs). The results showed that the BRAF (V600E) mutation was associated with extra-thyroidal extension (OR = 2.09, 95 % CI = 1.69-2.58), advanced TNM stage (OR = 1.90, 95 % CI = 1.62-2.22), lymph node metastasis (OR = 1.68, 95 % CI = 1.41-2.01), multifocality (OR = 1.22, 95 % CI = 1.06-1.40), and recurrence (OR = 2.50, 95 % CI = 1.73-3.59). The meta-analysis suggested the potential roles of BRAF (V600E) mutation in pathological features. BRAF (V600E) might provide prognostic and diagnostic information for papillary thyroid carcinoma.