Objective Students’ academic success is crucial for families, educators, and the community. Specific learning disorder reduces students’ academic performance and makes education difficult. Because of the rising prevalence of learning disorders (especially dyscalculia), it is necessary to pay more attention to dyscalculia, its diagnosis, and assessment to develop new interventions and scientific strategies to reduce symptoms. Negative consequences of math problems in early childhood probably affect the individual and social aspects of life until adulthood. As far as we know, most children with dyscalculia have significant problems in executive functions, so the application of effective educational methods on executive functions will improve cognitive functions and learning. The present study was conducted to determine the effectiveness of a cognitive rehabilitation program on the executive functions of students with dyscalculia. Materials & Methods This research was a quasi-experimental study with a pre-test-post-test design with a control group. The statistical population consisted of all 8 to 12 years old students who were studying in specific schools for learning disorders in the 2020-2021 academic year in Sanandaj City, Iran. Thirty children (17 boys and 13 girls) were selected by convenience method and assessed using the Iranian Key Math Test. Then, 28 students with one standard deviation lower than the mean (≤85 points) were diagnosed as dyscalculic, and their parents signed a written consent form. Students were excluded if they had seizures and epilepsy, or other neurodevelopmental disorders or were absent more than two times from intervention sessions. All students were matched according to gender and age and randomly assigned to the experimental (7 boys and 7 girls) and control groups (8 boys and 6 girls). The executive functions of all students were assessed by the Behavioral Rating Inventory for Executive Functions (BRIEF). The experimental group individually participated in 12 sessions (twice a week; 30 to 45 minutes per session) and was trained by the cognitive rehabilitation program. However, the control group only attended the mainstream curriculum. Again, all students were assessed by the BRIEF in the last session and 5 weeks later in the follow-up. The obtained data were analyzed by using analysis of variance with repeated measures. Results The findings showed that the cognitive rehabilitation program has significantly influenced executive functions and their components (behavior regulation and metacognition) in students with dyscalculia. According to the eta quotient, 42%, 32%, and 43% of the variances of executive functions, behavior regulation, and metacognition of the experimental group, respectively, have been explained by participating in the cognitive rehabilitation program. In addition, the program’s effectiveness lasted for a 5-week follow-up later. Conclusion Considering the effectiveness of cognitive rehabilitation programs on executive functions, designing and implementing the same rehabilitative programs not only improves the executive functions of students with dyscalculia but also prevents their problems relating to learning academic skills.