During the Jacobite rising of 1745 Hugh Mackay supported the British-Hanoverian Government and was Captain of the 2nd Mackay Independent Highland Company that fought at the Skirmish of Tongue on 25 March 1746, where money and supplies were captured from a French ship, and 156 Jacobites were taken prisoner. He also led his Independent Company at the Battle of Littleferry on 15 April 1746 where the Jacobites were again completely defeated. His Independent Company was also involved in the Raids on Lochaber and Shiramore. Later he was Lieutenant-Colonel of the 1st Sutherland Regiment.