Alterations to the auditory system’s structure and function may underlie the auditory processing and language disorders prevalent in autism spectrum disorder (ASD). This multimodal study compared DTI of the brainstem auditory pathway to magnetoencephalography (MEG) measures of auditory conduction velocity (M100 latency). The M100 latency measures the time between auditory stimulus and auditory cortex response. DTI and MEG were acquired from 29 children with ASD and 31 controls. Increased brainstem auditory pathway FA was predictive of faster signal conduction in controls (shorter M100 latency) (p<0.01), but not ASD. These results indicate ASD impacts the structure-function relationships throughout the auditory system.