•Hemodynamic activities were measured during and after catatonia using fNIRS.•Functional connectivity was low during catatonia.•Prefrontal functional connectivity increased after resolution of catatonia.•Prefrontal functional connectivity may serve as a novel marker of catatonia. Catatonia is a syndrome that manifests in patients with mental disorders and general medical conditions. However, functional changes to the brain that cause catatonia remain unknown. In the present study, we used functional near-infrared spectroscopy (fNIRS) to assess spontaneous hemodynamic activities in the brain at the times of onset and resolution of catatonic symptoms in patients with catatonia. We used 22-channel and 49-channel fNIRS to examine hemodynamic activities in the prefrontal cortex (PFC), and both frontal and parietal cortices, respectively. A total of ten patients who were diagnosed with catatonia were included in the study. Resting state measurements were taken for five minutes at the time of the onset and resolution of catatonic symptoms. Analyses were performed for the prefrontal region and the motor cortex within the parietal-frontal region of the brain. Functional connectivity between the cerebral hemispheres was evaluated systematically based on spontaneous oscillation of ΔHbO2. In the PFC, the resting state functional connectivity (RSFC) was significantly lower in the catatonic state than in the eyes-closed non-catatonic state (p = 0.047). The study demonstrated that the RSFC in the PFC, measured using fNIRS, may be an objective indicator of the change in catatonic symptoms.