Genetic variations within oncogene are frequently detected in many kinds of malignancies, including papillary thyroid carcinoma (PTC). Rs712 within 3'-untranslated region (UTR) of KRAS and BRAF rs3748093 have been reported to influence expression and function of the two genes. So we speculated that the two SNPs would implicate in activation of the two genes and increase disposition to PTC. For this, a hospital-based case-control study, including 330 PTC cases and 364 healthy check-up controls, was carried out to investigate the association between them. Our results showed that no significant association was found between BRAF rs3748093 and KRAS rs712 and risk of PTC in co-dominant, dominant, recessive, over-dominant and allele models in overall and subgroups. However, genotype TA and allele A of rs3748093 were significantly associated with TNM II stage, node and distant metastasis, respectively. And there were positive associations between genotype GT and allele T of rs712 and poor differentiation in cases. These findings suggested that rs3748093 and rs712 were involved in progression of PTC rather than risk, genotype TA and allele A of rs3748093 and genotype GT and allele T of rs712 could be emerged as poor prognostic factors for PTC in Chinese population. With limitation of our study, well designed, multiple centers and larger sample size case-controls studies are of great value to validate our findings.