Cognitive deficits in tasks involving the prefrontal cortex such as working memory or verbal fluency are a key component of schizophrenia. This led to the hypofrontality hypothesis of schizophrenia, which is widely accepted even though molecular underpinnings are elusive. While disturbances of glutamatergic neurotransmission might play a role, other components have rarely been investigated. Recently, the promoter region of nitric oxide (NO) synthase-I (NOS-I, encoded by the gene NOS1), impacting on prefrontal glutamate transmission, has repeatedly been associated with schizophrenia. We thus tested whether an associated schizophrenia risk variant (rs41279104), leading to reduced expression of the transcript, influences prefrontal brain functioning. Forty-three patients suffering from chronic schizophrenia and 44 controls were genotyped for NOS1 rs41279104 and investigated by means of functional near-infrared spectroscopy (fNIRS), while completing a working-memory task (2-back test) and a verbal fluency test (VFT). After matching for genotype, behavioural and brain activation data of 26 patients and 28 comparable controls were correlated to rs41279104. Healthy controls showed significant activation of large parts of the lateral prefrontal cortex during both tasks, whereas task-related changes in oxygenation were significantly reduced in patients. Schizophrenia patients also performed worse in both tasks. The NOS1 schizophrenia risk genotype rs41279104 AA/AG was associated with slower reaction time in the 2-back task, as well as with reduced right-hemispheric activation of the frontal cortex for VFT in patients only. Our fNIRS data extend previous studies suggesting disturbed prefrontal functioning in schizophrenia and suggest that genetic variation of NOS1 has a role in cognitive dysfunction, probably by mediating glutamatergic tone.