We provided the dataset of preprocessed diffusion tensor imaging (DTI) metrics [fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD)] from 43 patients with post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (PI-ME/CFS), 33 patients with gradual onset ME/CFS (GO-ME/CFS), and 66 healthy controls (HCs) with sedentary lifestyles. The dataset can be used to replicate the results of the manuscript titled “Opposite white matter abnormalities in post-infectious vs. gradual onset chronic fatigue syndrome revealed by diffusion MRI.” This manuscript investigated white matter microstructural abnormalities in PI-ME/CFS and GO-ME/CFS using DTI and their correlation with clinical symptoms. Details of data collection and processing can be found in the manuscript. The demographic and symptom scores were provided in the spreadsheet. Four subject-level datasets were determined: 1. DTI_AD.nii.gz: preprocessed axial diffusivity; 2. DTI_FA.nii.gz: preprocessed fractional anisotropy; 3. DTI_MD.nii.gz: preprocessed mean diffusivity; 4. DTI_RD.nii.gz: preprocessed radial diffusivity.