Previously, schizophrenia is found to be related to the variability of the functional magnetic resonance imaging (fMRI) signal in the white matter. However, evidence about the relationship between genetic vulnerabilities and physiological fluctuation in the brain is lacking. We investigated whether familial risk for psychosis (FR) and polygenic risk score for schizophrenia (PRS) are linked with physiological fluctuation in fMRI data. We used data from the Oulu Brain and Mind study (n = 140-149, aged 20-24 years) that is a substudy of the Northern Finland Birth Cohort 1986. The participants underwent a resting-state fMRI scan. Coefficient of variation (CV) of blood oxygen level dependent (BOLD) signal (CVBOLD) was used as a proxy of physiological fluctuation in the brain. Familial risk was defined to be present if at least one parent had been diagnosed with psychosis previously. PRS was computed based on the results of the prior GWAS by the Schizophrenia Working Group. FR or PRS were not associated with CVBOLD in cerebrospinal fluid, white matter, or grey matter. The findings did not provide evidence for the previous suggestions that genetic vulnerabilities for schizophrenia become apparent in alterations of the variation of the BOLD signal in the brain.