Background: The after-school period is potentially a “critical window” for promoting physical activity in children. The purpose of this study was to qualitatively explore children’s perceptions of the factors influencing their engagement in physical activity during the after-school period as the first phase in the development of a questionnaire. Methods: Fifty-four South Australian children age 10–13 years participated in same gender focus groups. Transcripts, field notes, and activity documents were analyzed using content analysis. Through an inductive thematic approach, data were coded and categorized into perceived barriers and facilitators according to a social ecological model. Results: Children identified a number of factors, including safety in the neighborhood and home settings, distance to and from places, weather, availability of time, perceived competence, enjoyment of physical activity, peer influence, and parent influence. New insights into bullying and teasing by peers and fear of dangerous animals and objects were revealed by the children. Conclusions: In this study, hearing children’s voices allowed the emergence of factors which may not be exposed using existing surveys. These findings are grounded in children’s perceptions and therefore serve as a valuable contribution to the existing literature, potentially leading to improved intervention and questionnaire design.