The present study using near-infrared spectroscopy examined the neuronal correlates of Japanese long/short vowel contrast discrimination and its relationship with behavioral performance by comparing native Japanese (L1) subjects and Korean subjects learning Japanese as a second language (L2). Phoneme-specific responses were predominantly observed in the left auditory area only in the L1 subjects, although the behavioral scores of the L2 subjects indicated categorical perception (CP) that was indistinguishable from that of the L1 subjects. These inconsistent relationships were more evident in the correlation coefficients between the brain recording and behavior. However, slower reaction times and non-specific brain responses in the L2 listeners suggest differences in their cortical processes from those of the L1 subjects. These findings suggest that the CP of L2 phonemes as determined by behavioral scores alone does not always predict a language-specific neural processing as employed by the L1 listeners.