Lipton received a B.A. in biology from C.W. Post Campus of Long Island University in 1966 and a PhD in developmental biology from the University of Virginia in 1971. From 1973 to 1982, he taught anatomy at the University of Wisconsin School of Medicine, before joining St. George's University School of Medicine as a professor of anatomy for three years. Lipton has said that sometime in the 1980s, he rejected atheism and came to believe that the way cells function demonstrates the existence of God.
From 1987 to 1992, Lipton was involved in research at Pennsylvania State University and Stanford University Medical Center. Since 1993, he has been teaching in non-tenured positions at primarily alternative and chiropractic colleges and schools.
Lipton has said, "When I first started back in the '70s and my research was coming out, it was the golden age of genes. My research irritated a lot of people. I always thought of them as lemmings running off the cliff of DNA, and I'm standing there on the side with the results from my stem-cell studies thinking, 'Oh my God, you're all going the wrong way.' At some point I realised that they marginalised my work because it didn't conform to their conventional beliefs and I thought, well, they're not even being scientists. And I just left the system. I realised the message is more important for the average person than it is to argue in the halls of science".