The following article discusses Khomeini’s consideration for the existence of any relation between science and religion. The author deals with the importance of this matter and shows how the struggle of media for the alleged separation between the two is so divisive. The author also touches on the questions of the total independence of scientific thought and its clear separation from religion. He carries an interesting piece on Western forms of secularism. In another section, he analyzes Khomeini’s concept that had different interpretations. He argues the obstacles in the way of the growth of science and technology, its methodology and especially its limited perceptive knowledge and notes the contradiction between these. His analysis of the matter makes room to discuss how it can be created in an atmosphere where science and religion have harmony. This observation precisely insists on the Islamic view.