To date, there is an absence of curative treatment for very early onset schizophrenia. The antipsychotic drugs that are currently recommended have very little effect and are often badly tolerated by children. We report a case-study which results show a beneficial and significant efficacy of fMRI-guided rTMS in the treatment of pharmaco-resistant hallucinations. Moreover, rTMS applied over several cortical regions provided the means to reveal for the first time a functional dissociation between auditory-verbal hallucinations and agency impairments. These results demonstrate the efficacy of rTMS for young patients suffering from drug-resistant hallucinations but they furthermore question the physiopathology of the hallucinatory process by suggesting that agency and hallucinations may be sub served by different neural networks.