Introduction Metal ions are known to accumulate in the thyroid and some play an important role in the function and homeostatic mechanisms of the thyroid gland. Certain metal ions are known endocrine disruptors while others are classified to be carcinogenic. Although higher thyroid cancer incidences rates have been reported in regions with high metal levels in soil and drinking water, including volcanic regions, the effect of heavy metals on the thyroid is still poorly understood. To investigate the association between heavy metals and thyroid cancer, a comprehensive meta-analysis was performed to draw a more evidence-based conclusion for individual metal ions. Material and Methods Nineteen studies were included in this meta-analysis, of which 9 studies reported blood metal ion levels, 8 studies reported tissue metal ion levels and 2 studies reported blood and tissue metal ion levels. The standardized mean difference (SMD) was calculated between thyroid cancer patients group and a control group (benign thyroid patients group or healthy controls group) per study. Results A significant positive standardized mean difference (SMD) in manganese tissue levels between thyroid cancer patients and benign thyroid patients (SMD: 0.56 (95% CI: 0.16, 0.95)) and a significant negative SMD in cobalt blood levels between thyroid cancer patients and healthy controls (SMD: -2.03 (95% CI: -3.95, -0.10)) was found. No difference in levels of other metals in blood or thyroid tissue between thyroid cancer patients and non-thyroid cancer patients was noted. Discussion and Conclusion The present meta-analysis therefore demonstrates the urgent need for future studies, especially given the increasing exposure of the general population to various environmental pollutants, including metal ions, and the thyroid cancer burden worldwide.