The auditory brainstem response reflects neural encoding of the acoustic characteristic of a speech syllable with remarkable precision. Some children with learning impairments demonstrate abnormalities in this preconscious measure of neural encoding especially in background noise. This study investigated whether auditory training targeted to remediate perceptually-based learning problems would alter the neural brainstem encoding of the acoustic sound structure of speech in such children. Nine subjects, clinically diagnosed with a language-based learning problem (e.g., dyslexia), worked with auditory perceptual training software. Prior to beginning and within three months after completing the training program, brainstem responses to the syllable /da/ were recorded in quiet and background noise. Subjects underwent additional auditory neurophysiological, perceptual, and cognitive testing. Ten control subjects, who did not participate in any remediation program, underwent the same battery of tests at time intervals equivalent to the trained subjects. Transient and sustained (frequency-following response) components of the brainstem response were evaluated. The primary pathway afferent volley -- neural events occurring earlier than 11 ms after stimulus onset -- did not demonstrate plasticity. However, quiet-to-noise inter-response correlations of the sustained response ( approximately 11-50 ms) increased significantly in the trained children, reflecting improved stimulus encoding precision, whereas control subjects did not exhibit this change. Thus, auditory training can alter the preconscious neural encoding of complex sounds by improving neural synchrony in the auditory brainstem. Additionally, several measures of brainstem response timing were related to changes in cortical physiology, as well as perceptual, academic, and cognitive measures from pre- to post-training.