Duration-deviant mismatch negativity has been investigated as a potential biomarker for predicting early psychosis clinical outcomes. Although progressive mismatch negativity changes have been linked to neurodegeneration and cognitive decline after psychosis onset, it is unclear whether similar changes occur in patients at clinical high risk for psychosis. Therefore, we examined longitudinal mismatch negativity changes and their associations with cognition and functioning in 24 clinical high risk for psychosis individuals and 22 healthy controls. Participants underwent duration-deviant mismatch negativity recordings at baseline and the 1-2-year follow-up. Neurocognitive functioning was assessed via Trail Making Test parts A and B, and general functioning was measured with the Global Assessment of Functioning scale. Group differences in mismatch negativity amplitude change over time were evaluated using repeated-measures analysis of covariance, and its associations with cognitive and functional changes were assessed via Spearman correlations. Compared with healthy controls, individuals at clinical high risk for psychosis had significantly reduced mismatch negativity amplitudes at the FCz electrode site at baseline. However, there was no significant group-by-time interaction in mismatch negativity amplitude, nor were its changes significantly correlated with neurocognitive or general functioning changes, suggesting that progressive changes in duration-deviant mismatch negativity may not occur prior to psychosis onset in individuals at clinical high risk for psychosis. Given the heterogeneous outcomes in the clinical high risk for psychosis population, larger samples and longer follow-up durations are needed to elucidate the clinical significance of duration-deviant mismatch negativity in this group.