Project-based learning (PBL) combines student-centred learning with motor practice, but evidence on physical activity and motor performance in school physical education remains limited. This exploratory pilot study compared PBL with teacher-led instruction in two non-randomised cohorts comprising 53 girls: 27 fifth-grade pupils in basketball and 26 seventh-grade pupils in aerobics. Each cohort included one intact class per condition. Outcomes included pre–post basketball motor tests, final aerobics performance and physical activity records from subsets of pupils. Motor comparisons were exploratory, and wearable outcomes were summarised descriptively at the class and lesson levels. The baseline-adjusted obstacle dribble test comparison favoured the control class (experimental-minus-control difference: +4.01 s; 95% CI: 1.88 to 6.14; Holm-adjusted p = 0.002); the other two basketball comparisons remained inconclusive. The final aerobics score difference was −0.49 points on a 0–16 scale (95% CI: −3.75 to 2.78). Recorded running and walking differed little between basketball classes, while mean heart rate was lower in the experimental classes, especially in aerobics. Class membership was confounded with an instructional approach, preventing attribution of differences to PBL. The findings do not establish superior motor performance, equivalent outcomes or preservation of overall physical activity volume. Studies with multiple classes per condition and more complete measurement are needed.