Discrepancies between subjective cognitive difficulties and objective measures of cognitive function in people with MS have been identified and may be related to mood and fatigue. The aim of the present study was to examine associations of depression and fatigue with discrepancies between subjective and objective cognitive functioning in pwMS. 177 participants with MS attending a University Hospital Department of Neurology MS Outpatient clinic completed the Brief International Cognitive Assessment for MS (BICAMS), MS Neuropsychological Questionnaire (MSNQ), Hospital Anxiety and Depression Scale (HADS) and Modified Fatigue Impact Scale (MFIS). To quantify the discrepancy between objective (BICAMS) and subjective (MSNQ) cognitive functioning, discrepancy scores were calculated by subtracting MSNQ z-score from composite BICAMS z-score. Based on their discrepancy score, participants were grouped as ‘Underestimated’, ‘Overestimated’ and ‘Non-discrepant’. 39% of the total sample demonstrated poorer subjective cognitive functioning than their objective cognitive performance suggested (‘Underestimated’). 23% of the total sample indicated lower objective scores than their subjective report suggests (‘Overestimated’). 38% participants indicated relatively no discrepancy between objective and subjective cognitive measures (‘Non-discrepant’). Significant differences were observed between the discrepancy groups in terms of depression and fatigue, with the ‘Underestimated’ group demonstrating greater levels of depression and fatigue (ps < .01). Regression analysis indicated that cognitive fatigue and depression significantly contributed to variance in subjective cognitive functioning. Our findings suggest that subjective reports of cognitive function may be influenced by depression and fatigue, emphasising the importance of cognitive, mood and fatigue screening as part of routine clinical care.