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 = .001) and Class M (7.57 ± 5.79, p = .019) than for participants in Class N (0.76 ± 8.00). Mean change scores for reading (11.54 ± 7.51, p = .017) and total motor composites (6.12 ± 5.07, p = .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.