Background <p>The preventive effect of physical activity on the risk of thyroid cancer remains inconsistent and unclear. We investigated the association between physical activity and the risk of thyroid cancer using a meta-analysis of prospective cohort studies.</p> Methods <p>A systematic search of PubMed and EMBASE was conducted from inception till December 20, 2024. A pooled relative risk (RR) with its 95% confidence interval (CI) was calculated using an adjusted RR with its 95% CI from each study.</p> Results <p>A total of nine prospective cohort studies (<i>N</i> = 2 764 014 adults; incident thyroid cancer cases, 15 166) were included in the final analysis. In the meta-analysis of all the studies, highest physical activity was not significantly associated with the risk of thyroid cancer (RR, 0.91; 95% CI 0.76–1.09; <i>I</i>² = 56.5%), compared with lowest physical activity. Physical activity was statistically significantly associated with a decreased risk of thyroid cancer in the studies conducted in Asia (RR, 0.75; 95% CI 0.64–0.88; <i>I</i>² = 4.2%), but not in either Europe or North America. Also, physical activity was statistically significantly associated with a decreased risk of thyroid cancer in the studies published after 2015 (RR, 0.78; 95% CI 0.65–0.93; <i>I</i>² = 22.1) and the high-quality studies (RR, 0.81; 95% CI 0.70–0.94; <i>I</i>² = 5.2).</p> Conclusions <p>Physical activity decreased the risk of thyroid cancer in the studies conducted in Asia, published after 2015, and rated as having high methodological quality. Further high-quality prospective cohort studies are warranted to confirm our findings.</p>