In 1993, Surya Ganguli graduated from University High School in Irvine, California at the top of his class at the age of 16. He then attended the Massachusetts Institute of Technology, where he spent five years completing bachelor's degrees in mathematics, physics, and electrical engineering and computer science, as well as a master's degree in the latter. During that time, Ganguli assumed research positions at the Information Mechanics Group at the MIT Laboratory for Computer Science, at the Center for Space Research and the Center for Theoretical Physics at the MIT Department of Physics, and the Information Systems and Technologies Laboratory and the Dynamics of Computation Group at the Xerox Palo Alto Research Center.