A number of near-infrared spectroscopy (NIRS) studies in schizophrenia have shown that there is a significant dysfunction of the prefrontal cortex (PFC) in patients with schizophrenia, but it remains unclear how atypical antipsychotics affect the function of the PFC. To investigate the changes in brain activation patterns in schizophrenia who accepted antipsychotic treatment, we used NIRS to measure the hemodynamic changes of the PFC in patients with schizophrenia at the time of enrollment and after 4 weeks of treatment during a verbal fluency task (VFT). We included 16 schizophrenia and 17 sex- and age- matched healthy controls. Compared with the healthy controls, the VFT performance was significantly worse in patients with schizophrenia, as was the activation of the PFC. Furthermore, after 4 weeks of treatment, there was no significant improvement in VFT performance and the activation of the PFC in schizophrenia. Our results suggest that the function of the PFC and cognitive skills in schizophrenia were significantly impaired and do not improve from a short-term treatment of atypical antipsychotics.