Born in 1951 in Goshen, Indiana, Ainlay earned his bachelor's degree in sociology from Goshen College, and both his master's and Ph.D. from Rutgers University in 1981, with a thesis on "Intentionality, identity and aging: an inquiry into aging and adventitious vision loss".

He was appointed Director of the Center for Interdisciplinary and Special Studies in 1993, dean of the college in 1996, and finally vice-president for academic affairs in 1997.

Ainlay joined with five other college presidents and, with the help of the Andrew Mellon Foundation, created the New York Six Consortium.

In 2007, Ainlay was appointed by Governor Eliot Spitzer to the Commission on the Future of Higher Education in New York.

[4] Ainlay's sociological research projects have focused on investigations of blindness, aging, spirituality and various aspects of Mennonite life, all aimed at better understanding the ways in which people find meaning in their lives.