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Background Although perceptual interventions focus on sensory and cognitive skills, they significantly enhance the effectiveness of motor interventions by improving coordination, decision-making, and overall engagement in physical activities. A comprehensive literature review has demonstrated that incorporating perceptual interventions into motor exercises is beneficial. While there are several treatment strategies for SLD-diagnosed children, the potential role of goal-directed perceptual-motor exercises has not been studied. This study examined the effectiveness of goal-directed perceptual-motor training on attention, motor skills, and quality of life in children with Specific Learning Disorder (SLD). Methods This was a randomized clinical study with 38 children diagnosed with SLD between September 2021 and April 2022. The control group ( n  = 19) received a standard intervention protocol, and the intervention group ( n  = 19) additionally received a perceptual-motor training program. Bourdon Attention Test, the Bruininks-Oseretsky Test 2–Short Form (BOT2- SF), and the Pediatric Quality of Life Inventory (PEDSQL) were used as outcome measures. Results The intervention significantly improved attention, fine and gross motor skills, and life quality as evidenced by the within- and between-group comparisons at the end of therapy. Conclusions Goal-directed perceptual-motor physical training with cognitive aspects may enhance academic performance, social participation, and life quality for children with SLD by improving basic motor skills. Therefore, the inclusion of physical and task-specific perceptual-motor exercises in educational programs may offer several avenues for cognitive skill development in SLD children. Trial registration The protocol is retrospectively registered with http://clinicaltrials.gov/ (16/August/2023, Clinical Trial, NCT05998083).