This study investigated how Japanese learners of Korean perceive the similarity of stop sounds between the Korean and Japanese languages. The results found, compared to the beginner’s group, the advanced group showed a lower rating value for the similarity for the same stimulus sound, and the learners with a higher perception ability distinguished lower similarities, even among the inner groups of the beginner’s and advanced group. This study also investigated how the related information in the native language affects how the learners perceive lenis consonants in word-medial position in the Korean language, as Japanese stop sounds are divided into two sounds depending on [±voiced] feature, whereas Korean stop sounds do not have a voiced sound in word-initial consonantal context, but the lenis consonants go through voicing in word-medial position. In result, Japanese learners tend to perceive the lenis consonants in word-medial position much better than other sounds, and it was shown that the related information in native language had played a positive role in perceiving Korean word-medial consonants.