Objectives: The purpose of this study is to describe the genetic variants present in the Ecuadorian population and the incidence and mortality patterns of thyroid cancer in Ecuador from 2016 to 2021. Methods: The present research constitutes a nationwide cross-sectional study encompassing all reported cases of thyroid cancer (C-73) in Ecuador from 2016 to 2021. Incidence rates were calculated based on the annual population at risk, considering factors such as ethnicity, sex, age group, and the geographic location of the incidence. All data was collected from the Hospital Discharge Statistics and the Statistical Registry of General Deaths Databases. Results: Between 2016 and 2021, a total of 20,297 hospital admissions and 921 deaths attributed to thyroid cancer were reported in Ecuador. The incidence of thyroid cancer remained relatively stable from 2016 to 2019. However, there was a notable decrease in 2020, followed by an increase in 2021. Notably, thyroid cancer prevalence rates were found to be higher in highlands regions. Moreover, two genetic variants, the BRAFV600E and KITL678F, have been identified in the Ecuadorian population. It is noteworthy that women exhibited a higher susceptibility to thyroid cancer, being five times more likely than men to develop this condition. Conclusion: Ecuador exhibits one of the highest global incidences of thyroid cancer. Consequently, describing the genetic variants and epidemiological characteristics of thyroid cancer is imperative for enhancing healthcare access and formulating evidence-based public health policies. This research contributes towards a comprehensive understanding of thyroid cancer in the Ecuadorian context, aiming to improve targeted interventions and health outcomes.