There is an urgent need for the systematic monitoring of motor and cognitive neurodevelopment and the evaluation of motor skill development in infants and children with heart disease. Familiarizing students and early graduates with the developmental care needed by these patients may help in the system-wide implementation of early motor screening in this population. The purpose of this study was to investigate the agreement between a last-year physiotherapy student and an experienced pediatric physiotherapist when applying the Polish version of the Alberta Infant Motor Scale (AIMS) to a heterogenous group of children with congenital heart defects. Agreement between raters was verified based on the observation of 80 (38 females) patients with heart disease aged 1–18 months using a Bland–Altman plot with limits of agreement and an intraclass correlation coefficient. The bias between raters for the total score for four age groups (0–3 months, 4–7 months, 8–11 months and 12–18 months) was between −0.17 and 0.22 (range: −0.54–0.78), and the ICC was between 0.875 and 1.000. Thus, a reliable assessment of motor development or motor skills using the Polish version of the AIMS can be performed in pediatric patients with heart defects by clinically inexperienced last-year physiotherapy students who are familiarized with the AIMS manual.