Previous magnetic resonance imaging (MRI) studies reported increased brain gyrification in schizophrenia and schizotypal disorder, a prototypic disorder within the schizophrenia spectrum. This may reflect deviations in early neurodevelopment; however, it currently remains unclear whether the gyrification pattern longitudinally changes over the course of the schizophrenia spectrum. The present MRI study using FreeSurfer compared longitudinal changes (mean inter-scan interval of 2.7 years) in the local gyrification index (LGI) in the entire cortex among 23 patients with first-episode schizophrenia, 14 with schizotypal disorder, and 39 healthy controls. Significant differences were observed in longitudinal LGI changes between these groups; the schizophrenia group exhibited a progressive decline in LGI, predominantly in the fronto-temporal regions, whereas LGI increased over time in several brain regions in the schizotypal and control groups. In the schizophrenia group, a greater reduction in LGI over time in the right precentral and post central regions correlated with smaller improvements in negative symptoms during the follow-up period. The cumulative medication dosage during follow-up negatively correlated with a longitudinal LGI increase in the right superior parietal area in the schizotypal group, but did not affect longitudinal LGI changes in the schizophrenia group. Collectively, these results suggest that gyrification patterns in the schizophrenia spectrum reflect both early neurodevelopmental abnormalities as a vulnerability factor and active brain pathology in the early stages of schizophrenia.