This study examined differences in music perception between children with executive function deficits (EF deficits) and typically-developing children. The role of executive functions in music perception ability was also examined. Participants included 71 children (40 males), aged 9–11 years. The study utilized a between-subjects control group design in which executive functions were measured by the Behavior Rating Inventory of Executive Function (BRIEF), and music perception ability was measured by several music listening tasks of tone and timing discrimination. The children with EF deficits performed significantly poorer than their typically-developing peers when discriminating between duration of tones and when discriminating between rhythm patterns. However, pitch and melodic perception did not show performance decrement. The executive function of working memory was the only independent predictor of duration and rhythm perception ability as shown in multiple regression models. In conclusion, there are significant differences in duration and rhythm perception ability between children with and without executive dysfunction. Moreover, music perception testing may serve as a potential measure of executive functions assessment, and given that improvements in working memory are desirable for children with EF deficits, music-based activities may be a promising medium for working memory intervention.