Papillary thyroid cancers often occur as microcarcinoma. Some papillary thyroid microcarcinoma (PTMC) have been considered to be high aggressive according to advanced disease stages, extrathyroidal extension, and severe cervical lymph node metastasis. Although several factors are thought to predict the occurrence of aggressiveness from PTMCs, the origin of aggressiveness has been rarely studied. To answer this question, the correlation between BRAF(V600E) mutation and high aggressive PTMCs was investigated. The clinicopathological characteristic of totally 64 cases of PTMCs was investigated and the BRAF(V600E) mutational status of them was identified. BRAF(V600E) mutation was exclusively detected in PTMCs (37.5%). The data provided no correlation between the occurrence of BRAF(V600E) mutations and clinicopathological parameters, such as sex, age, and tumor-like lesions combination. The prevalence of BRAF(V600E) mutation of PTMCs with high aggressiveness (advanced disease stages, extrathyroidal extension, and nodal metastasis) was significantly higher (p < 0.05) than that of PTMCs without aggressive behavior. The BRAF(V600E) mutated PTMCs exhibited signs of higher aggressiveness than PTMCs without the mutation. BRAF(V600E) mutation may be a marker of high aggressiveness in PTMCs.