Professor Stork received a number of awards and honors including the following:
* 1957 Award in Pure Chemistry of the American Chemical Society
* 1959 Guggenheim Foundation Fellow
* 1961 Baekeland Medal, North Jersey ACS
* 1962 Harrison Howe Award
* 1966 Edward Curtis Franklin Memorial Award, Stanford University
* 1967 ACS Award for Creative Work in Synthetic Organic Chemistry
* 1971 Synthetic Organic Chemical Manufacturers Association Gold Medal
* 1973 Nebraska Award
* 1978 Roussel Prize, Paris
* 1980 Nichols Medal, New York ACS, Arthur C. Cope Award, ACS
* 1982 Edgar Fahs Smith Award, Philadelphia ACS
* 1982 Willard Gibbs Medal, Chicago ACS
* 1982 National Academy of Sciences Award in Chemical Sciences
* 1982 National Medal of Science from Ronald Reagan; Linus Pauling Award
* 1985 Tetrahedron Prize
* 1986 Remsen Award, Maryland ACS
* 1986 Cliff S. Hamilton Award
* 1987 Monie A Ferst Award and Medal, Georgia Tech.
* 1991 Roger Adams Award
* 1992 George Kenner Award, Liverpool
* 1992 Robert Robinson Lectureship, University of Manchester
* 1992 Chemical Pioneer Award, American Institute of Chemists
* 1993 Welch Award in Chemistry, Robert A. Welch Foundation
* 1994 Allan R. Day Award, Philadelphia Organic Chemists Club
* 1995 Wolf Prize, Israel
* 2002 Sir Derek Barton Gold medal, Royal Society of Chemistry
* 2005 Herbert C. Brown Award, American Chemical Society
Stork also held honorary doctorates from Lawrence University, the University of Wisconsin–Madison, the University of Paris, the University of Rochester, and Columbia University.
The inaugural Gilbert Stork Lecture was held in his honor in 2014 at his alma mater, the University of Wisconsin-Madison. Gilbert Stork named lecture series are also held at other institutions, including Columbia University and the University of Pennsylvania, as a result of his endowments.
He was fêted for his sense of humor and colorful personality by historian of chemistry Jeffrey I. Seeman who published a collection of "Storkisms".