The study examines the implications of religious intolerance on the Educational system in Nigeria. Nigeria experienced a lot of religious intolerance due to its diversity of ethnic groups and religions. Due to the narrow-mindedness, misunderstanding, extremism, and zeal of religious devotees, religion, intended to be a unifying element among many ethnic groups in Nigeria, has instead turned out to be one of the triggers destroying lives and property. Several persons have suffered bodily and psychological harm due to intolerance based on religious beliefs and practices, which has caused rifts between Nigerians of various religious backgrounds. Nigerian educational system is under threat from this turmoil. Problems of religious intolerance has hampered Nigeria's efforts to establish a standard educational system.