This study investigated the cognitive effect of a unified flag football program in young adults with intellectual disabilities (ID). Twelve participants practiced football drills with their typical peers for 50 min each session, twice a week for 15 weeks. Measures of three aspects of executive functions (e.g., verbal working memory, measured as digit span task; cognitive planning proficiency, measured as Tower of London task; and response inhibition, measured as Stroop color and word task) were tested before and after the program. Although the benefits in the digit span and Stroop tasks were not seen, participants with ID significantly improved performance in the Tower of London task. The cognitive benefits in executive function from this unified sport program were still evident. Our preliminary findings encourage individuals with ID to attend sport programs for mental health. In future studies, large sample size and additional supporting measures should be included to generalize the findings to the general population with ID.