This study aimed to investigate the performance on pair-matching tasks in children with Spinal Muscular Atrophy type I (SMA-I) and the relationship between this performance and motor function, functional independence and quality of life. SMA-I (n = 12; 6.0 ± 2.3 yrs; 9 boys, 3 girls) and control sex-, age-matched children (n = 12; 6.2 ± 2.6 yrs) performed four pair-matching figure, number and letter tasks. The eye tracker detected eye movements. SMA-I children were assessed with CHOP INTEND, Pediatric Evaluation of Disability Inventory, and Pediatric Quality of Life Inventory. Analysis of variance showed that SMA-I children had a lower percentage of correct answers and longer timed performance compared to controls (p < 0.05). Pediatric Evaluation of Disability Inventory score (social function domain) was correlated to the percentage of correct answers on the pair-matching tasks on task 1 (r = 0.81; p = 0.001) and task 2 (r = 0.66; p = 0.020). Pair-matching performance of SMA-I children was poorer than the performance of control children. There was a relationship between pair-matching performance and social function. The restricted interaction with the environment, due to severe paralysis and poor verbal communication, is associated with cognitive difficulties in SMA-I children. The eye tracker was helpful in cognitive assessment of SMA-I children, who responded to the cognitive tests with eye movements.