Korea introduced a new diagnosis-related group (NDRG), which is a mixed-bundle reimbursement system. We evaluated the effects of NDRGs on laboratory test quality by analyzing data over three years (2016–2018) from the Korean Association of External Quality Assessment Service (KEQAS). A total of 42 NDRG-participating hospitals (CASE), 84 non-participating similar size-hospitals (CON-1), and 42 tertiary hospitals (CON-2) were included. We assumed the proportion of KEQAS results with a larger than 2 standard deviation index (SDI) to be a bad laboratory quality marker (BLQM). CASE BLQMs were lower than CON-1 BLQMs for more than 2 years in alkaline phosphatase (ALP), alanine aminotransferase (ALT), chloride, glucose, sodium, and total protein, and higher in creatinine. CASE BLQMs were higher than CON-2 BLQMs for more than 2 years in ALP, chloride, creatinine, glucose, lactate dehydrogenase (LDH), phosphorus, potassium, sodium, total calcium, total cholesterol, triglyceride, and uric acid. Mean SDIs for general chemistry tests were not significantly different depending on NDRG participation. However, the NDRG is currently a pilot program that compensates the amount of each institution’s reimbursement based on the fee-for-service system, and most participants were public hospitals. Thus, the effects of NDRGs on laboratory test quality should be re-evaluated after the NDRG program has stabilized and more private hospitals are participating.