Background: The association between iodine levels and the risk of papillary thyroid cancer (PTC) has been suggested, but not definitively established. This study is to compare the iodine status of a group of patients with PTC (with and without BRAFV600E) with that of a healthy population cohort. Methods: A cohort of patients scheduled for thyroidectomy was enrolled, along with a community-based health-screening cohort with no known history of thyroid disease. Median urinary iodine (UI) levels, creatinine-adjusted median UI levels, and food frequency questionnaire (FFQ) scores (mean ± SD) were compared. In a subgroup analysis, these values were compared between BRAFV600E-positive and BRAFV600E-negative patients in the PTC group. Results: The PTC group consisted of 210 patients, and the control group consisted of 90 healthy individuals. Among the 191 PTC patients whose BRAFV600E mutational status was reported, 169 (88.5%) were revealed positive for the mutation. The median UI levels were significantly higher in the PTC group (786.0 μg/l) than the control group (112.0 μg/l; p < 0.001), as was the case with creatinine-adjusted median UI levels (884.6 μg/g creatinine versus 182.0 μg/g creatinine; p < 0.001) and FFQ scores (66.2 ± 17.5, range 13–114 versus 54.6 ± 21.5, range 16–134; p < 0.001). No significant differences were seen in the subgroup analysis between BRAFV600E-positive and BRAFV600E-negative patients. Conclusions: Our results indicate that iodine status differs significantly between patients with PTC and healthy controls, suggesting that iodine may be involved in the occurrence of PTC, although the association between iodine levels and BRAF mutational status did not reach statistical significance.