Liberal Democrat science spokesman Evan Harris has lost his seat in Oxford West and Abington to a Christian candidate.
One Christian group said his defeat was the “most significant individual result of the election”.
Dr Harris is well-known as a secularist campaigner and has a strong record in supporting gay rights, along with being the honorary president of the Liberal Democrats’ LGBT group Delga.
He was defending a majority of 7,683 but lost out to Conservative candidate Nicola Blackwood, who is a member of the Christian Conservative Fellowship.
She won 23,906 votes, while he won 23,730 votes.
Ms Blackwood, a first-time candidate, says she is concerned about the rights of religious people.
The Conservative Christian Fellowship website says: “Along with many Christians, she is concerned that right to freedom of religion is being undermined without proper understanding of the potential consequences for faith groups or the wider community.
“In particular, she fears that the voice of Christians and people of other faiths on key issues of conscience is too readily dismissed in public debate.”
During the election campaign, Mr Harris was criticised for his support of stem cell technology, euthanasia and abortion rights.
One leaflet circulated about him referred to him as “Doctor Death”.
Christian Concern for Our Nation, a religious group accused of being anti-gay, said his defeat was a “significant development for both Christians and the political world”.
Director Andrea Williams said: “This is the most significant individual result of the election as it sees the removal of one of the most prolific anti-life and anti-Christian parliamentarians.”
Keith Porteous Wood, the director of the National Secular Society, commended Dr Harris for his work.
He said: “Evan Harris has been a tireless worker for secularism and many other progressive causes during his time in parliament and we will miss his input enormously. Let us hope that he will have another opportunity to return to parliament in the not too distant future. We commiserate with him and deeply regret the loss of a brave and effective voice in parliament.”