Children with learning difficulties are commonly assumed to have underlying cognitive deficits by health and educational professionals. However, not all children referred for psycho-educational assessment will be found to have deficits when their abilities are measured by performance on cognitive tasks. The primary aim of this study was to estimate the prevalence of this inconsistent cognitive profile (ICP) in a transdiagnostic sample of children referred by health and education service providers for problems related to attention, learning and memory (N = 715). A second aim was to explore whether elevated mental health problems were associated with ICPs. Findings suggest that approximately half of this sample could be characterised as having an ICP. Cognitive difficulties, whether identified by parent ratings or task performance, were associated with elevated internalising and externalising difficulties. Crucially, a larger discrepancy between a parent’s actual ratings of a child’s cognitive difficulties and the ratings that would be predicted based on the child’s performance on cognitive tasks was associated greater internalising and externalising difficulties for measures of working memory, and greater externalising difficulties for measures of attention. These findings suggest that subjective cognitive difficulties occurring in the absence of any task-based performance deficits may be a functional problem arising from mental health problems.