As one of the main goals of Iranian Islamic Revolution, achieving a modern Islamic civilization derived from Islamic rationality is faced with some challenges. As the most fundamental for an intellectual system, such intellectual challenged can be named “rationality”. On this basis, using attributional analysis type of the qualitative research method, this paper is to answer the following question: “Based on the Islamic revolution leaders’ viewpoints and at the regional level, which most fundamental intellectual challenge does the Islamic revolution face on its way for achieving its depicted high level goals, i.e., bringing up a modern Islamic civilization, and how could they be overcome? The findings indicate that “Takfiri rationality” is the most fundamental challenge at the regional level. Challenge gaps between Takfiri rationality and Shia rationality at the region can be worded as “adhering to texts versus narrations”, “opposing the reason“, “monotheism and accusing Islamic sects”, “believing in and relying on the Prophet companions’ fairness” as well as “opposing emulation”. Criticizing such a rationality, Shia rationality emphasized on “monotheism in Shia school of thought and being free of superstition”, “emphasizing on the necessity of empowering the Islamic revolution and the Islamic axis of resistance”, “the necessity of annihilating ISIS as the main promoter of Islamophobia all over the world”, “opposing any kind of violence and act of terrorism” as well as “denying whatsoever kind of dividing Islamic sects”. Hereupon, operational solutions for dealing with the challenge of Takfirism are proposed in three categories, namely intellectual-scientific, cultural, political and military-security.