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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 cognitive deficits as measured by performance on neuropsychological tasks. The 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 psychological distress was associated with ICPs. Findings suggest that approximately half of this sample could be characterised as having ICP. Cognitive difficulties, whether identified by subjective reports or objective task performance, were associated with elevated internalising and externalising difficulties. Crucially, having a larger discrepancy between a subjective rating of cognitive difficulties and performance on objective cognitive tasks was associated with experiencing greater internalising and externalising difficulties. This study therefore suggests that subjective cognitive difficulties occurring in the absence of any objective performance deficits may be a functional problem arising from psychological distress and maladaptive emotional regulation tactics.