This research was conducted to reveal the differences between the intonation systems of Persian and Japanese languages and to be applied to the contrastive linguistics and language teaching fields. First,a description of the intonation system in the Autosegmental-Metrical Phonology framework was chosen as reference for each language. Based on these two descriptions, the intonations of the two languages were studied and compared, and finally one difference between the two systems was pointed out in a hypothesis. Data representing all tonal structures and intonational patterns of Persian and Japanese were then collected. Five Japanese students of Persian language and five Iranian students of Japanese language were asked to read the data in the lab environment. Analysis of pitch contours of the recorded utterances proved the established hypothesis that Persian language uses the nuclear pitch-accent while there is not such a phenomenon in Japanese.