National antimicrobial usage and prescription patterns during the 12 years from 2002 to 2013 were analyzed using the National Health Insurance Service-National Sample Cohort. Antimicrobial usage was analyzed by major illness, sex, age, area of residence, income rank, diagnosis, and type of medical institution for each year. Total antimicrobial prescriptions increased from 15.943 daily defined dose (DDD)/1,000 inhabitants/day in 2002 to 24.219 in 2013. In 2013, 72% of total prescriptions were administered in clinics. Antimicrobials were most frequently prescribed to children younger than 10 years, followed by adults aged 70 years or older and those aged 60–69 years. Penicillins and cephems were the most popular classes of antimicrobial used. In 2013, 48% of total antibiotic usage (11.683 DDD/1,000 inhabitants/day) was due to respiratory diseases. After the Korean government has implemented a series of healthcare policies, antibiotic prescription decreased for the treatment of upper respiratory infection, the causative agents are mostly viruses.