This study aimed to evaluate the effects of a neuropsychopedagogical motor intervention program (NMIP) on the cognitive functioning and academic achievement of students. 201 students aged 7 to 10 participated, randomly assigned to either the control group (103 students underwent two assessments during the NMIP period) or the experimental group (98 students underwent NMIP interspersed with two assessments). The NMIP utilized the Coordinating Methodology, focusing on motor development, executive functions, and mindfulness. It consisted of 36 sessions, each lasting 15 minutes, involving the coding and decoding of figures and colors with parts of the glass human body, implemented by the class teacher in the school setting. Cognitive functioning and academic achievement were assessed using the Children's Scale for Inhibitory Control Screening (CSICS), Neuropsychopedagogical Scale for Working Memory Screening (NSWMS), Scale for Screening Phonological Abilities (SSPA), and Children's Scale for Reading and Writing Screening (CSRWS) before and after the NMIP. The results showed significant improvements in the experimental group: ±19% (p<0.01) in CSICS, ±29% (p<0.01) in NSWMS, ±23% (p<0.01) in SSPA, and a reduction of ±52% (p<0.01) in reading and writing difficulties measured by CSRWS. Additionally, ANOVA analysis indicated superior performance (p<0.01) in cognitive functions and academic skills among children in the experimental group post-NMIP compared to those in the control group. In conclusion, the NMIP demonstrated substantial positive effects on both cognitive functioning and academic achievement in elementary school students.