The majority of patients with papillary thyroid carcinoma (PTC) have an excellent prognosis, but some show poorer outcomes and would benefit from adjunctive prognostic tools. The B-Raf proto-oncogene, serine/threonine kinase (BRAF) mutation, either based on both its presence or its quantitative measurement, and ultrasound (US) features may serve as a prognostic marker. The aim of this study was to investigate (1) the association between clinical-pathologic prognostic factors and the BRAF mutation found in fine-needle aspirates, based on both its presence and its corresponding cycle threshold (Ct) value, and (2) the association between prognostic factors and suspicious US features classified by the thyroid imaging reporting and data system (TIRADS) in PTC.Two-hundred fifty-eight consecutive patients with PTC > 1 cm and who underwent preoperative US-guided fine-needle aspiration were included in this retrospective study. Clinical-pathologic variables were compared between patients with and without the BRAF mutation. Multivariate analyses were performed to investigate (1) the association between clinical-pathologic prognostic factors and the BRAF mutation found in fine-needle aspirates, based on both its presence and corresponding Ct values, and (2) the association between prognostic factors and suspicious TIRADS US features.BRAF-positive patients had a higher proportion of multiple tumors (P = 0.017). The number of suspicious US features classified by the TIRADS was an independent factor for predicting lateral lymph node metastasis, both in all 258 patients (odds ratio [OR] = 1.902, P = 0.005) and in 214 BRAF-positive patients (OR = 1.686, P = 0.037). The BRAF mutation status or BRAFCt values were not associated with any of the clinical-pathologic prognostic factors.In conclusion, a higher number of suspicious US features classified by the TIRADS, but not the BRAF mutation, are associated with lateral lymph node metastasis in patients with PTC, and can aid in the preoperative identification of patients at increased risk of lateral lymph node metastasis.