Objectives This population-based study aimed to collect, analyze, and summarize the long-term trends in medical imaging use in Taiwan. Methods A retrospective cohort population-based study of medical imaging usage for the individuals who received care under the National Health Insurance system from 2000 to 2017. CT and MRI utilization rates were determined overall as well as across certain variables including patient age, hospital type, health care type, hospital characteristics, and geographic area. Results Individuals registered in our health insurance system have received 21,766,745 CT scans and 7,520,088 MRI scans from 2000 to 2017. Annual growth rates for both imaging types were positive over that period, though growth rates have slowed in recent years. The growth rate for CT use was greatest (9–12%) between 2001 and 2004, dropped to 2% in 2005, then generally rose thereafter, reaching 3% in 2017. Similarly, MRI use growth peaked at 24% between 2001 and 2003, dropped to 4% in 2005, then increased in a fluctuating manner, reaching 2% in 2017. Conclusion Over the past 2 decades, CT and MRI use in Taiwan has increased sharply, especially in the oldest age group (≥ 60 years old), but growth rates have slowed in recent years. Increases in imaging use have corresponded with improved clinical outcomes, including greater life expectancy and reduced mortality rates, though further assessment is required to demonstrate a direct link with imaging. Nevertheless, the better clinical outcomes are also predisposed by the comprehensive care covered by the NHI system. Key points CT and MRI use in Taiwan has elevated prominently in the two past decades, particularly in the elderly adults (≥ 60 years old). The growth rates have moved to a slower pace in recent years. The escalation of medical imaging utilization has been correlated with elevated clinical outcomes.