Background: Body representation is described as a fundamental ability to build efficient motor skills. However, no structured and evidence-based program on body representation currently exists. This study assesses the effectiveness of a school-based body representation program (ENCOR: EN for ‘Enfant’ and COR for ‘Corps’ in French) on body representation abilities and motor skills in preschool children. ENCOR focus on body representation abilities as a foundational ability for motor skills. It was designed with teachers and occupational therapists to be autonomously achieved by teachers. Methods: Twenty-three children aged 5–6 years were included and provided with education interventions (control versus ENCOR). Results: Body representation accuracy and precision in localization increased by about 20% and 37%, respectively, in the intervention program compared to the control intervention. In the body part naming task, participants performed fewer of the most frequent errors (i.e., from 198 to 116 left-right discrimination errors). As expected, performance in the body representation tasks and the motor skills tasks were correlated at baseline. We show that motor skills improved after the ENCOR training. Conclusions: Given the need for evidence-based programs in schools, this program could efficiently help implementing body representation education on a large scale. Future studies should evaluate the effectiveness of the program on other cognitive abilities and academic outcomes.