Purpose To investigate the potential effects of MRI protocols on brain FDG uptake in simultaneous PET/MR imaging. Methods Seventy healthy subjects and ten patients with temporal lobe epilepsy were enrolled. Healthy subjects were divided to three groups to undergo different PET/MR scan protocols: "continuous MRI" with MRI stimulation presented during the whole scan, "late MRI" with MRI stimulation started after 40 min glucose uptake, and "no MRI" without MRI stimulation at all. Region-wise and voxel-wise differences in FDG uptake among the three protocols were compared. All epilepsy patients were scanned with the "continuous MRI" scan protocol. The effects of MRI protocol stimulation on pathological interpretation were evaluated. Results Highest global averaged metabolism was found in the normal dataset with continuous MRI scan protocol (P <0.05). Specifically, we observed higher FDG uptake in the primary auditory cortex, putamen, and lower FDG uptake in the occipital lobe and cerebellum during the "continuous MRI" scan protocol. However, MRI protocol stimulation after 40 min glucose uptake did not cause any significant differences in FDG uptake. Respectively compared to the normal dataset, patients with epilepsy showed consistent hypometabolism in the temporal lobe. Besides, significant metabolism changes in the primary auditory cortex, vermin, and occipital lobe were found in the "late MRI" protocol. Conclusion The effects of MRI protocol on brain FDG uptake were varied. The effects, including from other practical setting, were conspicuous for scans where MRI protocol started immediately after glucose uptake, but would dramatically decrease to negligible 40 min later. Hence, it would be necessary for pathology studies to collect data from a normal control group using the same scan protocol for unbiased evaluation.