In the contemporary era, cognitive warfare has emerged as a new instrument for influencing public opinion and shaping collective behavior within societies. In this context, the Islamic governance system, grounded in religious foundations, assigns special importance to the Jihad of Clarification as a means of countering cognitive warfare. This study, adopting a descriptive–analytical approach and relying on library-based research, seeks to analyze the position and strategic role of the Jihad of Clarification in the sphere of Islamic governance for countering cognitive warfare, based on the intellectual framework of the Supreme Leader of the Islamic Republic. The analysis has been conducted using thematic analysis with the assistance of MAXQDA software. The findings of the study indicate that cognitive warfare has been one of the most significant challenges facing Islamic societies in recent decades. From the perspective of Islamic governance, the most effective strategy to counter cognitive warfare is the implementation of the Jihad of clarification. Based on the organizing themes of the discourse’s function in cognitive warfare and its role in reproducing cultural and intellectual resistance, the strategic position of elites in explaining truth and maintaining social cohesion in the face of cognitive warfare is emphasized. Jihad of clarification is identified as the central axis of cultural confrontation and a foundation for strengthening social resistance in cognitive warfare. Insight, courage, and enlightenment are presented as the fundamental components in countering distortion and cognitive warfare. The protection of Islamic identity through the clarification of the teachings and discourse of Ahl al-Bayt (the Prophet’s family) is viewed as essential in resisting cognitive distortions. Moreover, the psychological and cognitive analysis of cognitive warfare is considered necessary for  understanding its hidden layers and enabling an intelligent response.  From these discussions, the overarching theme — “The Jihad of Explanation as a Grand Strategic Framework of Islamic Governance for Countering Cognitive Warfare and the Distortion of Truth” — emerges. Within this framework, the role of the intellectual elite in articulating the Islamic discourse, engaging in cultural confrontation, and preventing distortion is identified as the main strategic approach.