Objectives: In France, cancer registries cover 20% of the population. The objective of this study was to estimate the incidence of thyroid cancer over the 2007–2011 period across all departments of metropolitan France using incidence data from registries and medical-administrative data. Method: A medical-administrative indicator, “AUP,” was constructed by cross-referencing data from the Program for the Medicalization of Information Systems (PMSI) and the Long-Term Conditions (ALD) registry. This indicator allows for the counting of individuals with cancer who were newly classified as having a long-term condition or who were hospitalized. Incidence estimates were calculated by adjusting departmental AUP data using the observed Incidence/AUP ratio in the registry area. The quality of the estimates was first evaluated in the departments of the registry area by comparing observed incidence with estimated incidence. Results: The preliminary evaluation step confirmed that the AUP/Incidence ratio could be used to estimate the departmental incidence of thyroid cancer. In France, the incidence estimated in this way for the 2007–2011 period showed significant variations between departments: the 5th and 95th percentiles of the distribution of age-standardized incidence rates across departments were 2.8 and 7.1 per 100,000 for men, and 8.3 and 21.2 per 100,000 for women. Areas of notable excess incidence were observed in certain departments in the Southeast and along the southwestern coast compared to the metropolitan average. Conclusion: This study confirms the extent of geographic disparities in thyroid cancer incidence among French departments and illustrates the value of cross-referencing data from medical and administrative databases to estimate departmental cancer incidence.