Increasing mental health issues, such as emotional problems, pose a threat for the academic performance of undergraduate students. We propose a route connecting emotional problems and academic performance through executive functioning skills (EFS). Despite the abundance of research on the topic of EFS, there is a significant gap in understanding this route, specifically among a population of undergraduate students. The aim of this study was to examine whether EFS mediated the association between emotional problems and academic performance among undergraduate students. Cross-sectional data (n = 2,531) was used from a survey among Dutch undergraduate students from a large variety of faculties at a university of applied sciences. We assessed emotional problems using the Depression Anxiety Stress Scale-21, five EFS (cognitive inhibition, task initiation, sustained attention, planning, time management), and academic performance (study delay; yes/no). Mediation analyses were performed, using the Hayes PROCESS macro, adjusted for gender. We found that cognitive inhibition, task initiation, sustained attention, planning, and time management mediated the association between emotional problems and academic performance. Regarding separate EFS, no large differences were found. The data suggests that improving all EFS in undergraduates experiencing emotional problems could be a fruitful strategy for preventing academic delays.