Integrated positron emission tomography (PET)/magnetic resonance imaging (MRI) could simultaneously obtain both functional MRI (fMRI) and F-18-fluorodeoxyglucose (FDG) PET and thus provide multiparametric information for the analysis of brain metabolism. In this study, we aimed to, for the first time, investigate the interplay of simultaneous fMRI and FDG PET scan using a randomized self-control protocol. In total, 24 healthy volunteers underwent PET/MRI scan for 30-40 min after the injection of FDG. A 22-min brain scan was separated into MRI-off mode (without fMRI pulsing) and MRI-on mode (with fMRI pulsing), with each one lasting for 11 min. We calculated the voxel-wise fMRI metrics (regional homogeneity, amplitude of low-frequency fluctuations, fractional amplitude of low-frequency fluctuations, and degree centrality), resting networks, relative standardized uptake value ratios (SUVr), SUVr slope, and regional cerebral metabolic rate of glucose (rCMRGlu) maps. Paired two-sample t-tests were applied to assess the statistical differences between SUVr, SUVr slope, correlation coefficients of fMRI metrics, and rCMRGlu between MRI-off and MRI-on modes, respectively. The voxel-wise whole-brain SUVr revealed no statistical difference (P > 0.05), while the SUVr slope was significantly elevated in sensorimotor, dorsal attention, ventral attention, control, default, and auditory networks (P < 0.05) during fMRI scan. The task-based group independent-component analysis revealed that the most active network components derived from the combined MRI-off and MRI-on static PET images were frontal pole, superior frontal gyrus, middle temporal gyrus, and occipital pole. High correlation coefficients were found among fMRI metrics with rCMRGlu in both MRI-off and MRI-on mode (P < 0.05). Our results systematically evaluated the impact of simultaneous fMRI scan on the quantification of human brain metabolism from an integrated PET/MRI system.