This study examines whether the inequality between universities is increasing in terms of research output, in the context of the New Public Management (NPM) regime based higher education reform in South Korea. Recent reforms in higher education sectors around the world illustrate a number of characteristics of NPM, with performance-based funding standing out among others. Performance-based funding has brought up several concerns, especially with unintended consequences of the reforms such as a widening gap in the research activities of universities. We provide an exploratory case study of the South Korean higher education system where performance-based funding programs are rampant, using a novel panel dataset comprised of all the general four-year universities (n = 184) in 2009-2015. The descriptive analysis of the temporal trend of research output inequality among universities shows that the answer of whether the gap is widening or not depends greatly on the use of indices of inequality. We report the conflicting results between the 'relative' and 'absolute' inequality index when applied to the dataset. Our findings are followed by the discussion on the measurements of inequality and their axioms regarding the institutional Matthew effect, suggesting more consideration on the nature of the data and the context.