After graduating Master of Arts from Street Andrews in 1588, he studied civil law at Paris, became ambassador to the Emperor, and held other court offices.
He appears to have been well known to his literary contemporaries in Scotland and England. He became court poet to the queen of King James I and VI. He wrote poems in Latin, Greek, and English, and was one of the first Scots to write in standard English. His major work was Diophantus and Charidora.
Inconstancy Upbraided is perhaps the best of his short poems.
He is credited with a little poem, Old Long Syne, which probably suggested Robert Burns"s famous Auld Language Syne. He is also the author of a ballad called "Bothwell" about the battle fought by James Hepburn, 4th Earl of Bothwell with the border reiver, John Elliot of Park, also known as Little Jock Elliot or Little Jock of the Park.
The ballad recounts how Bothwell, in attempting to arrest Little Jock Elliot, suffers life-threatening wounds, though he ends by slaying his foe. Ayton was eight years old at the time Bothwell perished in a dungeon in Denmark, and hence must have heard about the attempted arrest of Elliot by people familiar with the story, particularly as Bothwell was a figure of national renown.
This latter ballad (of indeterminate age) also implicitly states that Little Jock Elliot survived the encounter with Bothwell.
Aytoun is buried in the Ambulatory Chapels of in Westminster Abbey.