Kobayashi came to the United States as a recipient of the Orson Desaix Munn Fellowship of Princeton University and completed a PhD degree in electrical engineering in 1967. He worked for the IBM Thomas J. Watson Research Center at Yorktown Heights, New York, for fifteen years. He was a research staff member in its Applied Research Department from 1967–1970. He worked on seismic signal processing, data transmission theory, digital magnetic recording, and image compression algorithms, and then became Manager, Senior Manager, and Department Manager in its Computer Science Department from 1971–1982. He was a visiting professor at the University of California, Los Angeles, University of Hawaii, Stanford University, Technische Universität Darmstadt, and Free University of Brussels. He was appointed the founding director of the IBM Japan Science Institute in 1982, and served in that position until 1986, when he joined Princeton University's faculty as Dean of the School of Engineering and Applied Science, and the Sherman Fairchild University Professor of Electrical Engineering and Computer Science. He was Dean from 1986–1991, and was responsible for establishing multiple interdisciplinary and/or inter-institutional centers and programs in academic disciplines as material science, opto-electronics, earthquake engineering, surface engineered materials, discrete mathematics for computer science, and plasma etching. After finishing his tenure as Dean, he was an NEC C&C visiting professor at the RCAST, the University of Tokyo. Since the fall of 1992 until June 2008, he assumed a full-time research and teaching position at Princeton University's Department of Electrical Engineering. He was a BC ASI Visiting Fellow at the University of Victoria in Canada from 1998–1999. He retired from Princeton University in June 2008. He was a distinguished researcher at the National Institute of Information and communications technology of Japan in 2008–2016.
Commendation List for Outstanding Teaching, School of Engineering and Applied Science, Princeton University
2005: Life Fellow of IEEE
2005: Technology Award from Eduard Rhein Foundation of Germany, with Dolivo and Eleftheriou, for their contributions for their pioneering contributions to PRML, which allowed dramatic increases in the storage capacity of computer hard disks.
2006: Guest speech at the Entrance Ceremony of the University of Tokyo, Graduate School
2012: C&C Prize from NEC Foundation, Japan for his "pioneering and leading contributions both to the invention of high-density and highly reliable digital recording technology and to the creation and development of a performance-evaluation methodology for computer and communication systems."