Musicians are highly trained to discriminate fine pitch changes but the neural bases of this ability are poorly understood. It is unclear whether such training-dependent differences in pitch processing arise already in the subcortical auditory system or are linked to more central stages. To address this question, we combined psychoacoustic testing with functional MRI to measure cortical and subcortical responses in musicians and non-musicians during a pitch-discrimination task. First, we estimated behavioral pitch-discrimination thresholds for complex tones with harmonic components that were either resolved or unresolved in the auditory system. Musicians outperformed non-musicians, showing lower pitch-discrimination thresholds in both conditions. The same participants underwent task-related functional MRI, while they performed a similar pitch-discrimination task. To account for the between-group differences in pitch-discrimination, task difficulty was adjusted to each individual's pitch-discrimination ability. Relative to non-musicians, musicians showed increased neural responses to complex tones with either resolved or unresolved harmonics especially in right-hemispheric areas, comprising the right superior temporal gyrus, Heschl's gyrus, insular cortex, inferior frontal gyrus, and in the inferior colliculus. Both subcortical and cortical neural responses predicted the individual pitch-discrimination performance. However, functional activity in the inferior colliculus correlated with differences in pitch discrimination across all participants, but not within the musicians group alone. Only neural activity in the right auditory cortex scaled with the fine pitch-discrimination thresholds within the musicians. These findings suggest two levels of neuroplasticity in musicians, whereby training-dependent changes in pitch processing arise at the collicular level and are preserved and further enhanced in the right auditory cortex.