He won the Royal Medal in 1997 "In recognition of his contribution to our understanding of the way in which chemicals move from the living biosphere to the fossil geosphere, in particular the origin, genesis, maturation and migration of oil which has had great repercussions on the petroleum industry.",
He was a co-winner of the Dan David Prize in 2008 for his studies of organic chemical fossils, which reveal the inhabitants and climates of ancient worlds. (He shared the prize with Ellen Moseley-Thompson and Lonnie G. Thompson). 
The Eglinton reaction is named after him.