This study analyzed academic achievement gaps based on regional size and income level using a hierarchical linear model with data from the first to fifth waves of the 2013 Korean Education Longitudinal Study. The results showed that students attending schools in rural areas had lower academic achievement than those attending schools in metropolitan city. Specifically, the analysis of academic achievement in the first grade of middle school revealed that achievement in English and mathematics was significantly lower in rural areas than in metropolitan city. In the analysis of academic achievement growth rates, the growth rate of Korean language achievement in rural areas was lower than that in metropolitan city. Furthermore, the analysis of the interaction effects between regional size and household income showed that the influence of household income on academic achievement varied depending on the region. In metropolitan city, higher income levels were associated with higher academic achievement, but the opposite pattern was observed in rural areas. These findings suggest that the intersection of region and socioeconomic status can exacerbate educational disparities within specific groups.