Abstract Objective To examine the relationships between intraindividual cognitive variability (IIV) and self-reported cognitive and functional difficulties in persons with multiple sclerosis (pwMS). We hypothesized higher perceived cognitive and functional difficulties would be associated with higher IIV. Method Participants (n = 35) were pwMS from a prospective memory intervention study. During the baseline evaluation, participants completed an objective neuropsychological test battery and a self-report measure of cognitive functioning (Perceived Deficits Questionnaire; PDQ Total). Participants were asked if they had problems in eight different functional areas due to their memory, with the number of endorsed problems summed. Two measures of IIV, an intraindividual standard deviation (ISD) score and maximum discrepancy score (MDS), were created from 11 indices. The relationship between the IIV and PDQ were assessed with individual linear regressions, controlling for demographics and disease-related characteristics, while Spearman correlations examined the associations with the number of reported functional memory problems. Results The PDQ was not significantly associated with either the ISD (b = −0.03, 95% CI: −0.15, 0.10, p = 0.672) or MDS (b = −0.01, 95% CI: −0.51, 0.32, p = 0.645). The overall number of functional memory problems was correlated with both the PDQ (ρ = 0.40, p = 0.018) and ISD (ρ = −0.35, p = 0.039), but not MSD (ρ = −0.22, p = 0.201). Conclusion(s) Perceived cognitive dysfunction was not associated with IIV. However, self-reported functional problems with memory were associated with perceived cognition, as well as one metric of IIV. ISD may better reflect moment to moment fluctuations that lead to difficulties with daily functioning, as opposed to MDS which may reflect underlying variation (e.g., base rates of impairment) in cognitive performance.