Purpose This study was conducted to examine the atropine eye drop prescription trend for children diagnosed with myopia, and to determine the factors associated with the prescription of atropine eye drops. Design This was a population-based cross-sectional study. Methods This study was conducted using a national representative sample from the National Health Insurance (NHI) claims data. All school children between 4 and 18 years of age who had visited an ophthalmologist and were diagnosed with myopia between 2000 and 2007 were included herein. The main outcome measure was the proportion of subjects who were prescribed atropine eye drops in each year. Logistic regression was used to identify the factors associated with atropine eye drops being prescribed. Results The prescription of atropine eye drops for children diagnosed with myopia increased significantly from the school years 2000 (36.9%) to 2007 (49.5%). There was also a shift from prescribing high concentrations (0.5 and 1%) of atropine eye drops to lower concentration ones (0.3, 0.25, and 0.1%) within this period. Atropine eye drops were more frequently prescribed to 9-12-year-old children (OR ¼ 1.26-1.42, compared with those 7-8 years old), and to children from families with a high socioeconomic status (OR ¼ 1.19-1.25); however, they were less prescribed to those living in mid to low urbanized areas . Conclusions This study revealed an increasing trend of atropine eye drop prescription for children with myopia in Taiwan. Our study provides eye-care professionals worldwide a reference for the potential integration of atropine eye drops into their clinical practice toward children with myopia.