In a statement, Lunney said he's leaving voluntarily so as not to entangle his Tory colleagues in controversy over his beliefs regarding evolution.
He will sit as an Independent but continue to vote with the ruling Conservatives, he said.
Lunney's decision was sparked by reaction to remarks he made last month, which he says were inflated by the media and became part of a "firestorm of criticism and condemnation" surrounding two provincial politicians from Ontario and Alberta who do not believe in the theory of evolution.
"In a society normally proud of embracing difference, the role of the media and partisan politics in inciting social bigotry and intolerance should be questioned," he said.
Late last month, Lunney defended the two members, tweeting that he has no problem describing evolution as "scientific theory" but that people should stop calling it fact.
"(Beyond) realm of current science 2 observe or (reproduce) origins," he tweeted, echoing views he's previously expressed in the House of Commons that scientific fact can only be established "through the study of things observable and reproducible."
In Tuesday's statement, Lunney said he agrees with Christian groups who held a news conference last week to warn of "deliberate attempts to suppress a Christian world-view from professional and economic opportunity in law, medicine and academia."
"I share these concerns," Lunney said. "I believe the same is true in the realm of politics at senior levels."
Lunney, a chiropractor before being first elected in 2000, has said he does not plan to run again in the election scheduled for this fall.
Note to readers: This is a corrected story. An earlier version said both provincial politicians were from Ontario.