Mindfulness-based education (Mind-Edu) is increasingly being recognized as an effective educational approach to promote children’s social and emotional competence. Although it has been implemented in several schools in Thailand for many years, studies examining its impact on the developing brain have been scarce. We hypothesized that the Mind-Edu might have some effects on resting state brain activities in school-aged students; therefore, we investigated long-term effects of Mind-Edu on the EEG power spectrum and compared with the control. Participants are 53 typically developing children (27 girls) studying in the 6th grade, mean aged 11.7 years, SD = 0.4. They were divided into the Mind-Edu group (N = 22) and the control group (N = 31). These two groups are different in school curriculums. One school uses the Mind-Edu curriculum for all levels of education, and another one uses the country’s core curriculum. Electroencephalography (EEG) was recorded; eye-closed EEG segment was used for quantitative analysis and compared between groups. The results revealed that there was no significant difference between groups on the mean value of absolute beta, alpha, and delta powers over all electrode sites. However, the Mind-Edu group had a significant lower absolute theta power over the posterior brain regions and a significant smaller theta/beta ratio over the Cz electrode as compared to the control. Our results suggested that implementation of the Mind-Edu into the regular elementary school curriculum would be of benefit for enhancing maturation in brain areas involved with cognitive control and self-regulation, which might provide support for a smooth transition into the adolescence.