Human resources are pivotal for national development, yet Indonesia ranks 96th on the Human Capital Index (HCI), reflecting educational challenges. One of the educational problems in the Ministry of Education and Culture’s Strategic Plan and the National Medium Term Development Plan for 2020–2024 is the failure to achieve several targets for education system output indicators, namely the Gross Enrollment Rate and the Level of Completion of junior and senior high school level. These indicators can be achieved by measuring performance based on efficiency, making it essential to analyze the efficiency of the education system at those levels as an evaluation to help achieve the target output indicators for the education system. This study examines Indonesia’s education system efficiency from 2020 to 2022 across 34 provinces using Data Envelopment Analysis (DEA) and assesses changes over time with the Malmquist Productivity Index (MPI). Analysis reveals significant inefficiencies in junior and senior high school across regions. Dynamic efficiency analysis indicates a decline, particularly at the senior high school level, with North Kalimantan Province showing decreased efficiency due to policy changes. Aceh and North Sumatra exemplify regions achieving efficiency improvements at the junior and senior high school levels. The findings underscore the need for nationwide targeted policy interventions to enhance educational outcomes.