McKibben is the author of more than a dozen books on climate change and environmental issues.
He was honoured for his "mobilizing force to fight global warming", said the Sophie Foundation, which awards the $100,000 prize.
Born in 1960, McKibben set up the 350.org campaign in 2008 which led thousands of climate change demonstrations around the world.
He is also one of the leading opponents to the controversial pipeline project Keystone XL, aimed at transporting tar sands oil from the Canadian province of Alberta to refineries in Texas' Gulf of Mexico.
"This planet desperately needs a global mobiliser for change. Fighting immensely powerful interests McKibben has shown that mobilising for change is possible. This brings hope," the Sophie jury said.
The Sophie Prize was created by Norwegian author Jostein Gaarder, the author of the bestselling novel "Sophie's World", and his wife in 1997 and has been awarded 16 times.
It recognizes work for the protection of the environment.
Gaarder said the foundation's funds had now been depleted.
"This is how it was planned from the start," he told Norwegian news agency NTB.
"There are so many foundations that become so static, and we didn't want (the Sophie Prize) to become eternal," he said.
Previous prizewinners have included the international anti-globalisation organization Attac, Australian journalist John Pilger, late Kenyan environmentalist Wangari Maathai, ex-NASA climate scientist James Hansen and former French anti-corruption magistrate Eva Joly.
The 2013 prize will be awarded at a formal ceremony in Oslo on October 28th.