The auditory mismatch negativity (MMN) is a component of event-related potentials, which is being increasingly recognized as a candidate biomarker for early stages of psychosis. Although previous cross-sectional studies have demonstrated small MMN amplitude in early stages of psychosis, it remains unknown whether small MMN amplitude is due to progressive reduction during the early course. In this study, we investigated longitudinal changes of MMN in early stages of psychosis. Participant included 14 patients with first-episode psychosis (FEP), 16 individuals with ultra-high risk (UHR), and 16 healthy control subjects (HC). We measured MMN in response to duration deviants (dMMN) and that in response to frequency deviants (fMMN), respectively. The amplitudes of dMMN in FEP and UHR were significantly smaller in comparison to those in HC, which did not show a progressive decrease over time. The amplitude of fMMN did not differ among groups, which again did not show progression. There was no significant correlation between the length of the follow-up period and the longitudinal change of either deviant-type MMN in the FEP or UHR. These results suggest that dMMN is a trait marker in the early stages of psychosis, and that small dMMN amplitude in early stages of psychosis may reflect altered developmental process rather than progressive brain pathology. The amplitude of fMMN may not alter in early stages of psychosis. These findings may contribute to the future establishment of MMN as a biomarker in early stages of psychosis.