Background: Human beings firmly obtain a better understanding of the creator, its aims and destination, natural phenomena as well as the surrounding concepts with the help of thoughts. Invitation towards contemplation is one of the principles of Holy Quran's teachings. Thought is one of the best activities of the human being's brain from the neuroscience point of view, which occurs in specific parts of the cerebral cortex. These areas consist of parts of the cerebral cortex, which either does not exist in other creatures or is not highly developed. Objectives: The purpose of this study was to investigate the importance of thought from the Holy Quran's point of view and the Foundations of Neuroscience. Methods: This research was carried out during year 2015 in the city of Tehran (the capital city of Iran). In this qualitative study, data were collected based on the Holy Quran and the interpretation of authentic books of the Quran and matching interpretation of these verses with neuroscience articles and books in the field of thought. Results: Careful consideration of the data led to the identification of 18 verses of the Holy Quran that pointed directly to thinking, which were consistent with accepted principles in neuroscience. Conclusions: Scientific secrets of the Holy Quran can be easily revealed by making a connection between a medical sciences, basic sciences, and Quranic sciences. There is hope of greater connection between the community of researchers in different fields with Quranic scientists, which might lead to the discovery of the secrets of this scripture and deep realization of the mystery of permanence.