Roughgarden received a Bachelor of Science in biology and a Bachelor of Arts in Philosophy from University of Rochester in 1968 and a Ph.D. in biology from Harvard University in 1971. She is the author of 5 books and over 120 articles.

She came out as a transsexual woman at age 52. Prior to that time she was identified as a male named Jonathan Roughgarden. In essence, Jonathan Roughgarden left on sabbatical; Joan Roughgarden returned to the same job and title. On her return, she shed some administrative responsibilities.

Roughgarden has taught at Stanford University since 1972. She founded and directed the Earth Systems Program at Stanford and has received awards for service to undergraduate education. Roughgarden's current research links ecology with economic theory.

In addition to a seminal ecology textbook written with Paul R. Ehrlich, Roughgarden published a 2004 challenge to certain tenets of sexual selection titled Evolution's Rainbow (2004): this is not an attack on the central idea of natural selection; it is a proposed correction to Darwin's explanation of the mechanism of selection. Roughgarden rejects Darwin's sexual selection theory based on instances in which animals do not follow traditional sex roles where the male attempts to impress the female, and the female chooses her mate.This work also contains a literature survey on unexpected sexual behavior in many species of animals: homosexual behavior; several genders and two sexes in a species (in which a gender that never participates directly in reproduction still participates indirectly, thus affecting natural selection). Evolution's Rainbow served as a major inspiration for the Against Nature? exhibition. The book is noted for its outspoken negative attitude towards Darwin's theory of sexual selection.

An article published by her lab on these ideas received criticism in the pages of the journal Science. Forty scientists produced ten critical letters: one of the critical scientists said that the paper was "completely shoddy science and poor scholarship". However, Roughgarden, quoted as being "not altogether surprised" by the volume of dissent, argued that her team had replied to most of the criticisms.

In The Genial Gene (2009) the case against sexual-selection theory is continued and Social-Selection theory is presented as an alternative. It claims to explain a list of 26 phenomena which are not correctly explained by the current neo-Darwinian sexual-selection theory. The list includes phenomena such as sexual reproduction, the sperm/egg binary, male/female bodies, sex roles, sexual conflict, monogamy, homosexuality, the human brain, and human rape. According to Roughgarden, all answers in the neo-Darwinian sexual selection theory ultimately derive from a common view of natural behavior predicated on the selfish-gene concept, competition and deception, whereas the Social-Selection theory ultimately derives from teamwork, honesty, and genetic equality.

Roughgarden is also a Christian convert who has written on the relationship between Christianity and science. In her book Evolution and Christian Faith: Reflections of an Evolutionary Biologist, she reinterprets scripture passages commonly used to oppose evolution in order to emphasize her belief that the Bible does not conflict with evolutionary biology. The book further relates Christianity and evolution by saying that all life is interconnected, as members of a faith community are connected. Roughgarden opposes the theories of creationism and intelligent design, but asserts her belief in God's involvement in evolution. She attended and was a speaker at the Beyond Belief symposium in November 2006.