We used data from 13 cancer registries in China, Japan, and South Korea to analyze time trends in overdiagnosis of thyroid cancer between 1998 and 2012. Age-standardized and age-specific incidence and annual percentage changes were calculated. The number of thyroid cancers diagnosed and the proportion attributable to overdiagnosis were estimated, with calculations stratified by sex and age group. The Spearman method was used to analyze the correlation between thyroid cancer incidence and overdiagnosis. From 1998 to 2012, both the incidence and proportions of overdiagnoses of thyroid cancer in China, Japan, and South Korea showed an increasing trend, with higher rates in women than men. South Korea had both the highest incidence for men (10.1/10 ) and women (46.7/10 ) and the highest proportions of overdiagnosis (men, 90.3%; women, 94.9%). The fastest growth in overdiagnosis was in Chinese men and women (annual percentage changes 6.1 and 4.6, respectively). We found significant positive correlations between age-standardized incidence and proportions of overdiagnosis for both men (Spearman r = 0.98, p < 0.05) and women (Spearman r = 0.99, p < 0.05) in the three countries. Age-specific incidence curves in Chinese and South Korean individuals were of an inverted U-shape. Overdiagnosis of thyroid cancer in Japan was mainly concentrated in middle-aged and older patients, whereas in China and South Korea, it occurred primarily in the middle-aged. The incidence and overdiagnosis of thyroid cancer in China, Japan, and South Korea are increasing, necessitating the implementation of comprehensive measures to reduce these overdiagnoses.