Association of Southeast Asian Nation or ASEAN has been established in the year 1967 and it has been one of the successful regional organizations. ASEAN has used ASEAN Way as the doctrine to guide ASEAN member states in managing the regional cooperation. However, one of the approaches maintained by ASEAN which is ASEAN Non-Interference Principle has been questioned due to arising of humanitarian issues that happened in the region. The current study will examine the challenges ASEAN Non-Interference Principle in managing Rohingya issues from Malaysia perspectives. The core study will focus on Malaysia perspective as one of ASEAN members regarding the challenges of non- interference related to Rohingya issues. The sample of the study consists of five representatives from ministry of foreign affairs, National Human Right Commissioner for Refugees (UNHCR), Amnesty International Malaysia and Tenaganita as the respondents for the study. This study employs qualitative research method where interviews face by face and through email are conducted are used to investigate key objectives. The challenge of ASEAN Non- Interference Principle has given an effect on the Rohingya ethnic. This study suggests that the review on ASEAN Non- Interference Principle as the Rohingya issues do not affect internally but it has become regional issues. The issues have affected not only Myanmar but also other neighboring countries like Malaysia, Indonesia, Thailand and even Philippines. Thus, this principle needs to be adjusted in order to meet with twenty century situation (Severino, 2004).