Asymmetries in the perception of lexical tones have previously been reported in infant studies: the order in which certain tones are presented influences discrimination accuracy. Using disyllabic materials, the current study provides evidence that such asymmetries can be found for L2 learners of Mandarin Chinese as well, making their responses in identification and discrimination tasks qualitatively different from adult native speakers. Using an active oddball paradigm, we found that Tone 4 deviant within a Tone 1 standard environment was consistently easier to discriminate than the reverse condition. Furthermore, this difference is also reflected in amplitude differences of the auditory N2/P3 complex. In two subsequent EEG experiments, we systematically varied (a) the relative acoustic difference between standards and deviants and (b) stimulus variance within standards and deviants. Results indicated that both decreased acoustic difference as well as increased stimulus variance positively increase relative perceptual asymmetry as well as the relative difference between ERP responses. Finally, we compare multiple mechanisms by which the native/non-native pitch system might cause these perceptual asymmetries.