Japan’s Social Thinking and Academic Readiness Training (START) program Academic Readiness (AR) lesson aims to improve self-regulation, executive function, and behavior problems in kindergarten children, but the effects of the START program AR lessons in unfavorable circumstances are unclear. Therefore, this study investigated the effects of the START program AR lesson in affected areas after the Great East Japan Earthquake. A cluster randomized trial was conducted with 111 5-year-old children in two kindergartens in Miyagi Prefecture to evaluate the effectiveness of the six-week AR lesson. One kindergarten was randomly chosen to implement the AR lesson, and the other maintained standard education. In the intervention group, trained classroom teachers provided the children with a 20-min AR lesson once a week. Executive function, behavioral self-regulation, and internalizing and externalizing problem behaviors were measured before and after the six-week intervention. The intervention group showed improved inhibitory control and enhanced behavioral self-regulation compared with the standard practice group. In addition, teachers’ evaluations showed that children’s internalizing and externalizing problem behaviors improved significantly. The results indicate that the START program AR lesson was effective in enabling teachers to help students improve executive function, self-regulation, and problematic behaviors. Therefore, educators and policy-makers should consider implementing the START program AR lesson in kindergartens after a disaster.