Interest in the applications of mindfulness practice in education is growing in the scientific community. Recent research has shown that mindfulness practice in schools may be beneficial for executive functions (EFs) which are abilities crucial for healthy development. The study of the effects of mindfulness practices on children's neural correlates of EFs, particularly inhibitory control, may provide relevant information about the impact and mechanisms of mindfulness-based interventions (MBIs) in children. The aim of the present study was to investigate the effects of a MBI in elementary school children on the neural correlates of inhibitory control via a randomized controlled trial. Children from two 4th grade classrooms and two 5th grade classrooms located in a school identified as having low socioeconomic status in Santiago de Chile were randomly assigned to either receive a MBI or serve as active controls and receive a social skills program. Both before and after the interventions, electroencephalographic activity was recorded during a modified version of the Go/Nogo task in a subsample of children in each group. Additionally, teachers completed questionnaires of students' EFs and students completed self-report measures. Results revealed increases in EFs assessed by questionnaires together with improved P3 amplitude associated with successful response inhibition in children who received the MBI compared to active controls. These results contribute to the understanding of the ways in which mindfulness practices can promote the development of inhibitory control together with EF improvement, factors identified as critical for children's social and emotional development and positive mental health.