Background Delivering and monitoring residential rehabilitation services for pupils with acquired brain injuries (ABI) is challenging because of variability in aetiology, age and pre‐morbid characteristics. Therapists and educators in this residential rehabilitation setting identified the need for a comprehensive tool which would capture the pupils' ability to participate in typical, everyday, school‐based functional activities. This study aimed to explore the ability of the School Function Assessment (SFA) to identify levels of participation in school‐based functional tasks and demonstrate progress for pupils with an ABI in a residential rehabilitation setting. Methods The SFA was conducted on admission and discharge for pupils with ABI receiving residential rehabilitation between January 2007 and October 2011. Data analysis used Kruskal–Wallis to determine between‐group differences in age, time post injury and weeks in rehabilitation. Linear mixed effects modelling was used to establish differences between admission and discharge scores. Case vignettes demonstrated how the SFA was used with individual pupils. Results Seventy pupils were identified (31 traumatic brain injury; 29 non‐traumatic and 10 anoxic) 42 boys and 28 girls whose age at injury was 4.5–17.2 years (median 12.8). The SFA demonstrated that 54/70 pupils had made progress with their ability to participate in school activities. Significant differences were found between admission and discharge SFA scores for participation, physical and cognitive assistance and adaptation and activity performance (P < 0.05). There was wide variability between individual profiles reflecting the heterogeneity of ABI. Conclusions The SFA determined levels of participation in school‐based functional tasks for these residential pupils with an ABI and demonstrated progress both at the group and individual level in this residential rehabilitation setting. It identified the amount of support a pupil would need when they return to their local school and their strengths and needs in relation to participation in physical and cognitive school‐based functional activities.