Manual ability may be an important consideration when measuring cognition in children with CP because many items on cognitive tests require fine motor skills. This study investigated the association of fine motor dependent (FMD) and fine motor independent (FMI) items within the cognitive domain (COG) of the Bayley Scales of Infant Development—Third Edition (Bayley-III) and Manual Ability Classification System (MACS) in children with cerebral palsy. Children aged 2 to 8 (3.96 ± 1.68) years were included in this study. MACS levels were assigned at baseline. COG was administrated at baseline (n = 61) and nine months post-baseline (n = 28). The 91 items were classified into FMD (52) and FMI (39). Total raw score, FMD, and FMI scores were calculated. The association between MACS and cognitive scores (total, FMD, and FMI) were evaluated using linear regression and Spearman correlation coefficients. We found total, FMD, and FMI scores decrease significantly as the MACS level increases at the baseline. Both FMD and FMI scores decreased as MACS levels increased (worse function). There was a significant difference between the two slopes, with the FMD scores having a steeper slope. Similar patterns were observed nine months post-baseline. Children with lower manual ability scored lower in the cognitive domain at baseline and 9 months post-baseline. The significant difference in the performance of FMD items and FMI items across MACS levels with a steeper slope of changes in FMD items suggests fine motor skills impact cognition.