Little research has investigated the relationships among motor coordination, perceived physical self-concept (PSC), and physical activity during emerging adulthood. The purpose of this study was to investigate whether PSC mediates the relationship between motor coordination and moderate-to-vigorous physical activity (MVPA) in emerging adults. This was a cross-sectional study with 218 undergraduate students aged 17–23 years (167 females, 76.6%). Participants were asked to complete a questionnaire including self-reported measures of motor coordination, PSC and MVPA. The mediating effects of both overall and domain-specific PSC were tested on the relationship between motor coordination and MVPA. Motor coordination was found to have a significant indirect effect on MVPA through overall PSC. Exploratory analyses specifically showed a mediating effect of domain-specific PSC of activity on the relationships between motor coordination and MVPA during chores and leisure-time. Findings from the current study highlight the importance of PSC on the relationship between motor coordination and MVPA and showed that university students with poor motor coordination exhibit lower levels of PSC, specifically, the perception of activity. Future interventions targeting the enhancement of MVPA should focus on improvement in the self-perception of physical activity alongside motor skills training.