Background: The aim of this study was to investigate the expression of the BRAF V600E gene mutation and the RET/PTC gene rearrangement in the progression of papillary thyroid carcinoma (PTC) in 50 patients from Inner Mongolia. Material/Methods: Clinical data, blood, and tissue samples were obtained from 50 patients with PTC and ten patients with benign thyroid adenoma. Expression of BRAF V600E, RET/PTC, nuclear factor-kappa B (NF-kappa B), interleukin (IL)-1 beta, IL-6, tumor necrosis factor (TNE)-alpha, transforming growth factor (TGE)-1 beta, C-X-C motif chemokine ligand (CXCL)1, CXCL2, C-C motif chemokine ligand (CCL)2, and CCL3 were measured using polymerase chain reaction (PCR), immunohistochemistry, and an enzyme-linked immunosorbent assay (ELISA). Results: Of the 50 patients with PTC, 37 patients expressed the BRAFV600E gene mutation, eight patients expressed RET/PTC, and five patients showed concomitant BRAFV600E and RET/PTC. Time to recurrence for patients with PTC with BRAFV600E was significantly increased compared with patients with concomitant BRAFV600E mutation and RET/PTC rearrangement (P<0.05). Expression of BRAF V600E, RET/PTC, and concomitant expression of BRAFV600E and RET/PTC were significantly associated with patient age and lymph node metastasis (P<0.05). Serum levels of NE-kappa B, IL-1 beta, IL-6, TNF-alpha, TGE-beta and CCL3, and tumor tissue levels of IL-1 beta, IL-6, TNF-alpha, TGE-beta, CXCL2 and CCL2 in patients with PTC were significantly increased compared with patients with benign thyroid adenoma, before and after surgery (P<0.05). Conclusions: Expression of the BRAFV600E mutation and RET/PTC translocation promoted the activity of NE-KB, expression of inflammatory mediators, and lymph node metastases in patients with PTC.