Jewish, Kroto stated that religion never made any sense to him. He was a humanist who claimed to have three religions: Amnesty Internationalism, atheism, and humour. He was a distinguished supporter of the British Humanist Association. In 2003 he was one of 22 Nobel Laureates who signed the Humanist Manifesto.

In 2015, Kroto signed the Mainau Declaration 2015 on Climate Change