In the early phase of viral encephalitis, conventional MRI may appear normal. Diffusion-weighted imaging (DWI) is a sensitive tool for detecting early changes in cellular function in the central nervous system. To investigate the usefulness of DWI in the diagnosis of enterovirus 71 (EV71) encephalitis, and to determine whether DWI is superior to conventional MR sequences. MRI scans in 26 patients were retrospectively evaluated for distribution of lesions on T1-weighted images (T1WI), T2-weighted images (T2WI), fluid-attenuated inversion recovery (FLAIR), and DWI. Contrast-to-noise ratios (CNRs) were calculated for all regions on each sequence and differences in the four MRI sequences were assessed using CNRs. Apparent diffusion coefficient (ADC) values were measured for all regions to look for true restriction of diffusion. Fifteen out of 26 cases showed positive findings on MR imaging. The brain stem was involved in 11 patients, cortex and subcortical white matter in four patients. DWI was more sensitive in detecting the abnormalities (89.7%) compared to T2WI (48.7%), FLAIR (41.0%), and T1WI (35.9%), and the positive ratio of DWI was significantly higher compared to other sequences. Furthermore, no significant difference was found between T2WI and FLAIR (P = 0.649). The corresponding mean CNRs were 8.73 ± 2.57, 83.59 ± 29.28, 24.22 ± 6.22, and 132.27 ± 78.32 on T1WI, T2WI, FLAIR, and DWI, respectively. The absolute values of CNRs of lesions on DWI were significantly greater than those on other sequences. DWI appears to be more sensitive in detecting EV71 encephalitis than conventional MRI sequences. This capability may improve the accuracy in diagnosing EV71 encephalitis, especially at the early stage.