We report a case of schizophrenia with partial agenesis of the corpus callosum in a 14-year-old girl. Diagnosis of schizophrenia was confirmed in the longitudinal follow-up and partial agenesis of the corpus callosum was found on brain MRI at the prodromal stage of disease. The prodromal symptom was progressive deterioration of social and academic adjustment in a context of non-specified psychotic disorder in the father. We found no abnormality in the development but a history of seizures that did not require specific treatment. Follow-up at 8 months showed an increase in negative symptoms and the onset of delusional symptoms and disorganization leading to the prescription of antipsychotic treatment. A review of the literature shows that agenesis of corpus callosum is the most reliable brain morphology abnormality in schizophrenia and is related to the neurodevelopmental and abnormal brain connectivity hypothesis in schizophrenia. Although this abnormality may be a marker of disease severity, our case report highlights the lack of longitudinal follow-up to allow the characterization of a specific outcome pattern of schizophrenic adolescents with partial agenesis of the corpus callosum.