Congenital heart disease is defined as an abnormality in the cardiocirculatory structure or function. Various studies have shown that patients with this condition may present cognitive deficits. To compensate for this, several therapeutic strategies have been developed, among them, the LEGO® Education sets, which use the pedagogic enginery to modify cognitive function by didactic material based on mechanics and robotics principles. Accordingly, the goal of this study was to evaluate the effect of cognitive habilitation by using LEGO®-based therapy in pediatric congenital heart disease patients. This was a quasi-experimental study; eligible patients were identified, and their general data were obtained. In the treatment group, an initial evaluation with the neuropsychological BANFE-2 test was applied; then, once a week, the interventions were performed, with a final test at the end of the interventions. In the control group, after the initial evaluation, a second appointment was scheduled for the final evaluation. Our results show that >50% of children presented cognitive impairment; nevertheless, there was an overall improvement in treatment patients, showing a significant increase in BANFE scores in areas related to executive functions. LEGO®-based therapy may be useful to improve cognitive abilities; however, future research should be performed to strengthen the data.