BackgroundRare diseases (RDs) are difficult to diagnose and expensive to treat. Thus, the South Korean government has implemented several policies to help RD patients, including the Medical Expense Support Project, supporting low- to middle-income RD patients. However, no study in Korea has yet addressed health inequity in RD patients. This study assessed inequity trends in the medical utilization and expenditures of RD patients.MethodsThis study measured the horizontal inequity index (HI) of RD patients and an age- and sex-matched control group using the National Health Insurance Service data from 2006 to 2018. Sex, age, number of chronic diseases, and disability variables were used to model expected medical needs and adjust the concentration index (CI) for medical utilization and expenditures.ResultsThe HI index of healthcare utilization in RD patients and the control group ranged from -0.0129 to 0.0145, increasing until 2012 and fluctuating since then. This increasing trend was more apparent for inpatient utilization in the RD patient group than in the outpatient group. The same index in the control group ranged from -0.0112 to -0.0040 without a significant trend. The healthcare expenditure HI in RD patients rose from -0.0640 to -0.0038, showing pro-poor values but moving toward a pro-rich state. In the control group, the HI for healthcare expenditures remained between 0.0029 and 0.0085.ConclusionsThe HI of inpatient utilization and inpatient expenditures increased in a pro-rich state. The study results showed that implementing a policy that supports inpatient service utilization could help achieve health equity for RD patients.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12939-023-01903-9.