The aim of the present study was to investigate the executive function and planning features of students with different types of learning difficulties. Students with mathematics difficulty (MD; n = 17), reading difficulty (RD; n = 12), and their commonalities (MDRD; n = 22), along with typically academically developing peers (TD; n = 22), were evaluated on an array of cognitive measures (working memory, inhibition, and planning) individually. Results revealed significant differences among groups on various cognitive measures. Students in the MD, RD, and MDRD groups showed poorer performance compared to the TD group on all of the working memory, inhibition, and planning tasks. The MDRD group showed an overall weakness when compared to other groups, indicating severe cognitive deficits in students with MDRD. The RD group showed deficits in inhibition and planning on tasks requiring verbal skills; MD students showed deficits in inhibition and planning on digit-related tasks. However, no salient difference was found among the MD, RD, and TD groups on working memory. Results have implications for understanding the cognitive features of MD, RD, and MDRD. Intervention programs targeting inhibition and planning may be beneficial for improving reading and mathematics achievement in students with learning difficulties.