In previous studies, the effects of physically active academic lessons on academic achievement have been shown. Less is known about follow-up effects and the effects for disadvantaged groups. The first aim of this study was to examine 7-9 months follow-up effects of a physically active academic intervention on academic achievement. The second aim was to examine the effects of the 2-year intervention for a subgroup of socially disadvantaged children. A cluster-randomized controlled trial with 499 children (113 socially disadvantaged children) from second- and third-grade classes was conducted. Children's academic achievement was measured before the intervention started, after the first and second intervention year, and 7-9 months after the intervention ended. At the 7-9 months follow-up, the intervention group showed significantly greater gains in math performance in comparison with the control group. No significant follow-up effects were found on language performance. Furthermore, the lessons significantly improved the math and spelling performance of socially disadvantaged children after two intervention years. These children did not benefit more from the lessons than other children. In conclusion, effects of physically active academic lessons on math achievement persist when the lessons are no longer taught, and the lessons are an innovative way to improve the academic achievement of socially disadvantaged children. The findings suggest that physically active academic lessons should be considered for inclusion in school curriculums in order to improve the academic achievement of all children. Trial Registration: This study is registered at www.isrctn.com (No. ISRCTN17021806).