Despite the breadth of health benefits associated with regular physical activity (PA), many children in the UK are not sufficiently active enough to meet health guidelines, and tend to become less active as they mature into and throughout adolescence. Research has indicated that children’s school, home and neighbourhood environments can all significantly influence their opportunities to engage in moderate-to-vigorous physical activity (MVPA). However, less is known about how children’s MVPA patterns within these key environments may change across the school year. The current mixed-methods case study aims to explore this issue by tracking key stage 2 (KS2) and key stage 3 (KS3) children’s MVPA patterns across the school year. Fifty-eight children (29 boys, 29 girls, KS2 = 34, KS3 = 24) wore an integrated global positioning systems (GPS) and heart rate (HR) monitor over four consecutive days in the first term of school (autumn), before these measurements were repeated in the two remaining school terms (winter–summer). A subsample of children (n = 6–8 per group) were invited to take part in one of six focus groups each term to further explore their PA behaviours and identify the barriers and facilitators to PA. The children’s MVPA was significantly lower (p = 0.046) in term 2 (winter/spring term) than during the warmer terms (autumn and summer). All the locations showed reductions in MVPA in term 2, except indoor MVPA, which increased, and MVPA on foot in the neighbourhood, which remained consistent. Focus groups revealed location, friends, and the variety of options to be associated with MVPA, and poor weather, parental permission, and time limitations to be barriers to MVPA. This mixed-methodological, repeated-measures design study highlights differences in the activity patterns and perceptions of children over the school year. Future studies should implement longitudinal, multi-method approaches to gain deeper insight into how children’s PA behaviours differ over time. Consequently, this can inform future health policies promoting children’s PA throughout the year.