Spafford attended the State University of New York at Brockport, graduating with a double major in mathematics and computer science in three years.

[1] During the formative years of the Internet, Spafford made significant contributions to establishing semi-formal processes to organize and manage Usenet, then the primary channel of communication between users, and to defining the standards of behavior governing its use.

He is executive director emeritus of Purdue's Center for Education and Research in Information Assurance and Security (CERIAS), and founded its predecessor, the COAST Laboratory.

As a PhD advisor, Spafford supervised development of the Open Source Tripwire tool coded by his student Gene Kim.

He was also graduate advisor to Dan Farmer who coded the freeware Computer Oracle and Password System (COPS) tool.