The Islamic Revolution commenced with Imam Khomeini’s monumental organizational efforts and the training of revolutionaries. This auspicious tree, capable of nurturing and fostering human potential, entered universities in the form of Islamic student organizations. Ayatollah Khamenei, with a deep and futuristic understanding, has always sought to preserve and comprehensively upgrade these human-building and talent-fostering entities in universities. Through informal education, Islamic organizations install the “value software” in individuals and teach them the customs of individual and social life; therefore, utilizing the findings of modern educational sciences is essential for them. The main purpose of this research is to extract the most significant educational principles and methods of Islamic student organizations, based on the axiological foundations of Ayatollah Khamenei’s perspective. Utilizing a documentary method and qualitative content analysis—covering a purposive sample of Ayatollah Khamenei’s organizational works, as well as bylaws and organizational documents influencing these entities—the relevant axiological foundations and educational goals were determined. Educational principles were deduced using a deductive method, and educational methods were inferred by utilizing these principles alongside findings from educational sciences. Some of the research findings include the following principles: strengthening religious foundations (methods: correction and providing insight, study, associating with scholars, discussion); removing obstacles to human-building freedoms (methods: critique and guidance, covering up and guiding members regarding unintentional errors); value-based elitism (methods: providing free practical fields, knowledge-enhancement workshops); fostering justice (methods: demanding justice, promoting simplicity); love and genuine address (methods: direct dialogue, intellectual persuasion, intimacy and socialization); responsibility (methods: holding jihadist camps, Jihad of Clarification); idealism (methods: discourse-building, inspiring hope, “fire at will”); devotion to Wilayat (method: role-modeling); spirituality (methods: individual self-purification, remembrance and repentance, collective self-purification); and enemy-recognition and opposing the enemy (methods: providing Quranic insight in confronting the enemy, skeptical outlook toward the enemy’s media stream, establishing relations with anti-hegemonic organizations globally). It is recommended that, for the implementation of the methods identified in this research, working groups and think tanks be established within the framework of these organizations, and educational measures be carried out step-by-step by formulating implementation stages for each method, tailored to the conditions of each university.