Sankaraachaarya popularized the advaita thought among students of philosophy and seekers of knowledge of the Self or Brahman or Atman. But he is criticized by Indian theistic schools like Visistaadvaita and dvaita philosophies as “prachchnna bouddha – follower of the Buddha in disguise”. This comment of theistic schools makes it worthy of comparing the advaitic and Buddhist schools of thought in relation to consciousness, world, Soonya, and other expressions between the two thought systems. This paper does such a comparison from cognitive science point of view and how the elements of Buddhism and Advaita thought enrich the modern scientific field of cognitive science. Also, a brief analysis is presented how the supplementary and complementary nature of the Upanishads, the Buddhism, the Jainism and the Shaddarsanas of Indian philosophic systems can be used to further the understanding of form, structure and function of human consciousness, mind and their functions.