How rates of thyroid cancer diagnosis were affected by the emergence of COVID-19 variants during the 2020 to 2021 era of the pandemic has not been described. To estimate the total number of undiagnosed cases of thyroid cancer, by histologic type, during the first 2 years of the COVID-19 pandemic (2020 and 2021) by comparing observed to expected incidence and to test for changes in size of cancer at incidence during the same period compared to prior years. This longitudinal study analyzed trends in thyroid cancer diagnoses from 2016 to 2021 among US adults using data from the Surveillance, Epidemiology, and End Results 22 (SEER-22) program database. Data analyses were performed in April to May 2024. Age-adjusted incidence rate per 100 000 US adults, changes in incidence, estimated number of undiagnosed cases, and mean cancer size. Absolute rates of overall thyroid cancer incidence in the first quarter of 2016 and of 2019 were 21.0 and 18.8 per 100 000, respectively. From 2020 through 2021, the quarterly rates were 17.3, 11.1, 17.2, 17.9, 17.4, 19.0, 17.1, and 17.3 per 100 000, respectively. The observed incidence of thyroid cancers decreased by 11% for papillary cancers 2 cm or smaller (risk ratio [RR], 0.89; 95% CI, 0.83-0.95), 14% for papillary cancers larger than 2 cm (RR, 0.86; 95% CI, 0.79-0.93), 8% for follicular cancers (RR, 0.92; 95% CI, 0.82-0.92), 10% for medullary cancers (RR, 0.90; 95% CI, 0.78-1.04), and 15% for anaplastic cancers (RR, 0.85; 95% CI, 0.68-1.07) from March 2020 to December 2021. Oncocytic cancers declined in incidence early in the pandemic, but rates returned to baseline or above through 2021 (RR, 1.15; 95% CI, 0.97-1.37). Extrapolated to the general US population, the total estimated number of thyroid cancer cases not diagnosed (expected minus observed) from March 2020 to December 2021 was approximately 10 200: 5400 papillary cancers 2 cm or smaller (95% CI, 2380-8530), 3700 papillary cancers larger than 2 cm (95% CI, 1660-5810), 600 follicular cancers (95% CI, -260 to 1550), 300 medullary cancers (95% CI, -110 to 720), and 190 anaplastic cancers (95% CI, -75 to 530). Mean size at diagnosis did not change significantly between 2016 and 2021 for any histologic type. This longitudinal study found that by the end of 2021, many thyroid cancers remained undiagnosed. These were predominantly small papillary cancers but also affected all histologic types except oncocytic. These deficits in diagnosis could produce a temporary increase in the rate of patients presenting with larger or more advanced stage cancers in the future, and consequently, temporary increases in population morbidity and mortality.