In 1995, he jointly set up the Vega Science Trust, a UK educational charity that created high quality science films including lectures and interviews with Nobel Laureates, discussion programmes, careers and teaching resources for TV and Internet Broadcast. Vega produced over 280 programmes, that streamed for free from the Vega website which acted as a TV science channel. The trust closed in 2012.
In 2009, Kroto spearheaded the development of a second science education initiative, Geoset. Short for the Global Educational Outreach for Science, Engineering and Technology, GEOSET is an ever-growing online cache of recorded teaching modules that are freely downloadable to educators and the public. The program aims to increase knowledge of the sciences by creating a global repository of educational videos and presentations from leading universities and institutions.
In 2003, prior to the Blair/Bush invasion of Iraq on the pretext that Iraq had weapons of mass destruction, Kroto initiated and organised the publication of a letter to be signed by a dozen UK Nobel Laureates and published in The Times.  It was composed by his friend the Nobel Peace Prize Laureate the late Sir Joseph Rotblat and published in The Times on 15 February 2003.
He wrote a set of articles, mostly opinion pieces, from 2002 to 2003 for the Times Higher Education Supplement, a weekly UK publication.
From 2002 to 2004, Kroto served as president of the Royal Society of Chemistry. In 2004, he was appointed to the Francis Eppes Professorship in the chemistry department at Florida State University, carrying out research in nanoscience and nanotechnology.
He spoke at Auburn University on 29 April 2010, and at the James A. Baker III Institute for Public Policy at Rice University with Robert Curl on 13 October 2010.
In October 2010 Kroto participated in the USA Science and Engineering Festival's Lunch with a Laureate program where middle and high school students had the opportunity to engage in an informal conversation with a Nobel Prize–winning scientist.
He spoke at Mahatma Gandhi University, at Kottayam, in Kerala, India in January 2011, where he was an Erudite special invited lecturer of the Government of Kerala, from 5 to 11 January 2011.
Kroto spoke at CSICon 2011, a convention "dedicated to scientific inquiry and critical thinking" organized by the Committee for Skeptical Inquiry in association with Skeptical Inquirer magazine and the Center for Inquiry.
He also delivered the IPhO 2012 lecture at the International Physics Olympiad held in Estonia.
In 2014, Kroto spoke at the Starmus Festival in the Canary Islands, delivering a lecture about his life in science, chemistry, and design.