Kroto was a "devout atheist" who thought that beliefs in immortality derive from lack of the courage to accept human mortality. He was a patron of the British Humanist Association. He was a supporter of Amnesty International. He referred to his view that religious dogma causes people to accept unethical or inhumane actions: "The only mistake Bernie Madoff made was to promise returns in this life." He held that scientists had a responsibility to work for the benefit of the entire species. On 15 September 2010, Kroto, along with 54 other public figures, signed an open letter published in The Guardian, stating their opposition to Pope Benedict XVI's state visit to the UK.
Kroto was an early Signatory of Asteroid Day.
In 2008, Kroto was critical of Michael Reiss for directing the teaching of creationism alongside evolution.
Kroto praised the increase of organized online information as an "Educational Revolution" and named it as the "GooYouWiki" world referring to Google, YouTube and Wikipedia.