1699 in Scotland

• Monarch – William II
• Secretary of State – James Ogilvy, 1st Earl of Seafield, jointly with John Carmichael, 1st Earl of Hyndford (from 31 January)

• 12 January – James Sutherland is appointed first Regius Keeper of the Royal Botanic Garden Edinburgh and first King's Botanist.
• 2 March – The Edinburgh Gazette is first published.
• July – Darien scheme: The colony of New Edinburgh on the Gulf of Darién is abandoned; the colonists set out to return to Scotland.
• September – Darien scheme: The second expedition to Darien sets sail, unaware of the failure of the first.
• 23 September – A total solar eclipse affects the North-East of the country, including Wick.

• 2 February – Hugh MacDonald, bishop (died 1773)
• 13 April – Alexander Ross, poet (died 1784)
• 17 April – Robert Blair, poet (died 1746)
• 19 April – John Farquharson, Jesuit (died 1746)
• 31 May – Alexander Cruden, Biblical scholar (died 1770 in London)

Date unknown

• John Dalrymple, Member of Parliament for Wigtown Burghs, 1728–34 (died 1742)
• William Ged, goldsmith, inventor of stereotyping (died 1782)

• 29 November – Patrick Gordon, general in the Russian Army (born 1635)

• Timeline of Scottish history