Ninian Cockburn (died 6 May 1579) was a Scottish soldier and officer of the Garde Écossaise, a company which guarded the French king. He had an ambiguous role in political relations between Scotland, France and England during the war of the Rough Wooing and the Scottish Reformation.
Ninian was the third son of William Cockburn of Ormiston, East Lothian and Janet Somerville. The name Ninian was used interchangeably with "Ringan." The Cockburn family had strong Protestant leanings; John Knox was the tutor of his nephew, and George Wishart was arrested at Ormiston.
Ninian married Elizabeth Kemp. She may have been a connection of Janet Sinclair, the nurse of Mary Queen of Scots, and Henry Kemp, who had been pursemaster to James V of Scotland. Ninian was paid for travelling in connection with the King's privy purse in 1540. Ninian may also have been Alexander Crichton of Brunstane's servant "Cockburn." Brunstane worked for Cardinal Beaton at this time. Brunstane's servant was sent to France by James V in March 1540 with royal insignia borrowed from the King's pursuivant Patrick Ogilvy.
Ninian was amongst those accused of the murder of Cardinal David Beaton in 1546, and he joined the Protestant garrison during the subsequent siege of St Andrews Castle. Ninian was summoned for treason on 10 June 1546. Ninian's older brother, John Cockburn of Ormiston was also accused of involvement in the murder. John was a prominent Protestant and also on good terms with England, having a licence to trade their during the war of the Rough Wooing. According to the Earl of Glencairn, Ninian was a spy during the siege for the Governor, Regent Arran.