Purpose The purpose of this study was to investigate whether alterations of regional neural function in children with diffuse intrinsic pontine glioma (DIPG) had manifested deficit in behavioral inhibition using resting-state functional MRI (rs-fMRI). Methods There were 17 participants with DIPG who took part in the study. Eight children were with deficit in behavioral inhibition, whereas the other 9 children did not obtain deficit in behavioral inhibition. Five healthy children with age, sex, and education matched to the study group also participated as the control group. These 3 groups underwent rs-fMRI, and the results were then converted to amplitude of low-frequency fluctuation (ALFF) data. Amplitude of low-frequency fluctuation data were further analyzed by single-factor analysis of variance comparing among 3 groups based on the whole brain levels. Amplitude of low-frequency fluctuation results were subjected to t test of voxel-wised comparison to derive the rs-fMRI brain function differences between the 2 DIPG groups. The Pearson correlation between ALFF values of abnormal regions found in 3 groups and the scores obtained according to the Child Behavior Checklist were analyzed. Results The 3 groups had shown significant differences in terms of the ALFF results, with the ALFF increased in several brain regions (P < 0.05, corrected with AlphaSim, clusters >59 voxels), which include left supramarginal gyrus, left dorsolateral superior frontal gyrus, right precentral gyrus, and right middle frontal gyrus. Participants with deficit in behavioral inhibition had shown significant differences (ALFF decreased) in several brain regions, including left dorsolateral superior frontal gyrus and right fusiform gyrus (P < 0.05, corrected with AlphaSim, clusters >123 voxels), whereas other brain regions had shown ALFF increased, including left supramarginal gyrus, left middle frontal gyrus, and right medial superior frontal gyrus (P < 0.05, corrected with AlphaSim, clusters >123 voxels). There was no significant correlation between ALFF values and Child Behavior Checklist scores (P > 0.05). Conclusions These findings of focal spontaneous hyperfunction and hypofunction, which correlate with deficit in behavioral inhibition processing, and the abnormal brain regions are considered to be inefficient (in regions of the brain that may relate to compensatory brain and behavioral functioning, and it may be that the brain region needs to exert extra energy to perform a task to the same degree as the control group) or inability (inability in a certain region, or underpowered), pointing to a pathophysiologic process in executive dysfunction.