Background Deep convolutional neural networks have demonstrated robust and reliable PET attenuation correction (AC) as an alternative to conventional AC methods in integrated PET/MRI systems. However, its whole-body implementation is still challenging due to anatomical variations and the limited MRI field of view. The aim of this study is to investigate a deep learning (DL) method to generate voxel-based synthetic CT (sCT) from Dixon MRI and use it as a whole-body solution for PET AC in a PET/MRI system. Materials and methods Fifteen patients underwent PET/CT followed by PET/MRI with whole-body coverage from skull to feet. We performed MRI truncation correction and employed co-registered MRI and CT images for training and leave-one-out cross-validation. The network was pretrained with region-specific images. The accuracy of the AC maps and reconstructed PET images were assessed by performing a voxel-wise analysis and calculating the quantification error in SUV obtained using DL-based sCT (PETsCT) and a vendor-provided atlas-based method (PETAtlas), with the CT-based reconstruction (PETCT) serving as the reference. In addition, region-specific analysis was performed to compare the performances of the methods in brain, lung, liver, spine, pelvic bone, and aorta. Results Our DL-based method resulted in better estimates of AC maps with a mean absolute error of 62 HU, compared to 109 HU for the atlas-based method. We found an excellent voxel-by-voxel correlation between PETCT and PETsCT (R2 = 0.98). The absolute percentage difference in PET quantification for the entire image was 6.1% for PETsCT and 11.2% for PETAtlas. The regional analysis showed that the average errors and the variability for PETsCT were lower than PETAtlas in all regions. The largest errors were observed in the lung, while the smallest biases were observed in the brain and liver. Conclusions Experimental results demonstrated that a DL approach for whole-body PET AC in PET/MRI is feasible and allows for more accurate results compared with conventional methods. Further evaluation using a larger training cohort is required for more accurate and robust performance.