The purpose of this study was to independently determine the levels of moderate-to-vigorous physical activity (MVPA) and self-determined motivation of both boys and girls as they participated in prolonged units of invasion games (i.e. 6–12 lessons) through two pedagogical models: direct instruction and the tactical games model (TGM). It was hypothesized that given the differences in domain interaction and lesson structure, both boys and girls would gain higher levels of physical activity (PA) and possess higher quality motivation during TGM-based lessons when compared to direct instruction lessons. Seventy-two children aged 11–12 years (42 boys, 30 girls) were randomly assigned to either a control or intervention group (TGM). Children wore RT3® triaxial accelerometers over a 12 week period to objectively measure time spent in MVPA. The System for Observing Fitness Instruction Time (SOFIT) tool was completed during each lesson to additionally assess lesson context information and teacher behaviour. SDT questionnaires were also completed, pre and post-intervention. Boys in the TGM condition displayed significantly higher levels of MVPA in both rugby and football activities in comparison to the control group although no significant differences in motivation were noted post-intervention. While girls in the TGM condition recorded comparable PA levels in the football sessions, they recorded significantly lower PA activity levels in the netball lessons. There were no significant differences in girls’ motivation post-intervention. It is recommended that future studies build on this research by continuing to examine PA and the quality of student motivation while using GCAs over prolonged unit lengths (i.e. greater than 12 lessons) using structural equation modelling techniques to assess the relationships between, and mediating influences of, SDT constructs on PA levels.