This study explored whether Year 1 school children exposed to a 12-week classroom-based gross motor program progressed differently than Year 1 children undertaking their regular school program in motor proficiency, mathematics, and reading outcomes. Fifty-five Australian Year 1 school children (25 boys, 30 girls, mean age 6.77 ± 0.40 years) were exposed to either (i) their normal school program (Class N) or (ii) a 12-week program comprised of gross motor circuits and physically active: a) reading lessons (Class R) or b) mathematics lessons (Class M). Motor proficiency and academic performance in mathematics and reading were assessed using the Bruininks-Oseretsky Test of Motor Proficiency (2nd Edition) and the Wechsler Individual Achievement Test--2nd Edition--Australian Standardised Edition, respectively. Differences in outcomes between classes following the 12-week program were assessed. Mean change scores for the mathematics composite were significantly greater for participants in Class R (9.61 ± 5.62, p = 0.001) and Class M (7.57 ± 5.79, p = 0.019) than for participants in Class N (0.76 ± 8.00). Mean change scores for reading (11.54 ± 7.51, p = 0.017) and total motor composites (6.12 ± 5.07, p = 0.034) were also significantly greater for participants in Class M than Class N (4.47 ± 3.50 and 0.82 ± 4.38 respectively). A 12-week classroom-based gross motor program may be beneficial for motor skill development and learning in Year 1 school children. This pilot evaluation may usefully inform future experimental studies to further investigate whether classroom-based motor skill programs have a beneficial effect on motor proficiency and academic outcomes in children in the early years of primary school.