Bainbridge began his academic career at the Choate Rosemary Hall preparatory school in his birth state of Connecticut. He matriculated at Yale University and Oberlin College before settling on Boston University, where he received his B.A. in sociology in 1971.

Bainbridge received his Ph.D. in sociology at Harvard University in 1975 and went on to study the sociology of religious cults. In 1976, he published his first book, The Spaceflight Revolution, which examined the push for space exploration in the 1960s. In 1978, he published his second and most popular book, entitled Satan's Power, which described several years in which Bainbridge infiltrated and observed the Process Church, a religious cult whose founders had been members of Scientology. The study was one of the last of this type of academic studies done before new rules were introduced restricting unregulated participatory observation and study.

After completing his doctorate, Bainbridge served as an assistant (1975-1980) and associate professor (1980-1982) of sociology at the University of Washington. During this period, he worked with departmental colleague Rodney Stark on the Stark-Bainbridge theory of religion. Upon returning to Harvard as a visiting associate professor of sociology (1982-1987), he co-wrote the books The Future of Religion (1985) and A Theory of Religion (1987) with Stark. As of 2013, their theory, which aims to explain religious involvement in terms of rewards and compensators, is seen as a precursor of the more explicit recourse to economic principles in the study of religion later developed by Laurence Iannaccone and others.

From this period until the 2000s Bainbridge published more books dealing with space, religion, and psychology. These included a text entitled Experiments in Psychology (1986), which included psychology experimentation software coded by Bainbridge. He also studied the religious cult the Children of God, also known as the Family International, in his 2002 book The Endtime Family: Children of God.

Bainbridge has also taught at Illinois State University (professor of sociology and anthropology; 1987-1990) and Towson University (professor of sociology and anthropology & department chair; 1990-1992). He then joined the National Science Foundation as the director of its sociology program (1992-1999) before holding a series of positions that prefigured his current appointment in 2006 as Co-Director of Cyber-Human Systems at the National Science Foundation.