Effective early education is essential for academic achievement and positive life outcomes, particularly for children in poverty. Advances in neuroscience suggest that a focus on self-regulation in education can enhance children’s engagement in learning and establish beneficial academic trajectories in the early elementary grades. Here, we experimentally evaluate an innovative approach to the education of children in kindergarten that embeds support for self-regulation, particularly executive functions, into literacy, mathematics, and science learning activities. Results from a cluster randomized controlled trial involving 29 schools, 79 classrooms, and 759 children indicated positive effects on executive functions, reasoning ability, the control of attention, and levels of salivary cortisol and alpha amylase. Results also demonstrated improvements in reading, vocabulary, and mathematics at the end of kindergarten that increased into the first grade. A number of effects were specific to high-poverty schools, suggesting that a focus on executive functions and associated aspects of self-regulation in early elementary education holds promise for closing the achievement gap.