*Tilden Lecturer of the Royal Society of Chemistry, 1981–82
*Elected a Fellow of the Royal Society (FRS) in 1990
*International Prize for New Materials American Physical Society, 1992 (with Robert Curl and Richard Smalley)
*Italgas Prize for Innovation in Chemistry, 1992
*Royal Society of Chemistry Longstaff Medal, 1993
*Hewlett Packard Europhysics Prize, 1994 (with Wolfgang Kraetschmer, Don Huffman and Richard Smalley)
*Nobel Prize in Chemistry, 1996 (shared with Robert Curl and Richard Smalley)
*Carbon Medal, American Carbon Society Medal for Achievement in Carbon Science, 1997 (shared with Robert Curl and Richard Smalley)
*Blackett Lectureship (Royal Society), 1999
*Faraday Award and Lecture (Royal Society), 2001
*Dalton Medal (Manchester Lit and Phil), 1998
*Erasmus Medal of Academia Europaea, 2002
*Copley Medal of the Royal Society, 2002
*Golden Plate Award of the American Academy of Achievement, 2002
*Order of Cherubini (Torino), 2005
*Foreign Associate of the National Academy of Sciences, 2007
*Kavli Lecturer, 2007
* National Historic Chemical Landmark, American Chemical Society, 2010.
* Citation for Chemical Breakthrough Award, Division of History of Chemistry, American Chemical Society, 2015
Kroto was made a Knight Bachelor in the 1996 New Year Honours list.
The University of Sheffield North Campus contains two buildings named after Kroto: The Kroto Innovation Centre and the Kroto Research Institute.