Jacobite rising of 1745 - 1746
Harry Munro's company was one of three in the process of being raised in the North when the Commander in Chief in Scotland, General Sir John Cope arrived at Inverness on 29 August. Harry's uncle George Munro, 1st of Culcairn met Sir John Cope and agreed that the Munros "should instantly take arms and join the King's troops" and the next day Harry brought in 200 of his men in three companies. These three companies were raised by Harry Munro himself, Hugh Munro of Teaninich and William Munro of Achany.
Harry joined Sir John Cope at the Water of Nairn and when the army marched for Aberdeen on 4 September Loudon's Highlanders regiment included his three companies, while George Munro of Culcairn's detachment acted as scouts. Sir John Cope remained in Aberdeen where a fourth company of Loudoun's regiment joined the others until 14 September from where they sailed to Dunbar and had their infamous defeat at the Battle of Prestonpans. Harry was among 70 officers taken prisoner and for a time was imprisoned in Glamis Castle but by mid January 1746 he was among 31 men released who arrived at Edinburgh, where he learnt the news of the deaths of his father Robert and his uncle Duncan after the Battle of Falkirk (1746).
Meanwhile, the main body of Munros having escorted Sir John Cope successfully to Aberdeen had returned to the north under George Munro, 1st of Culcairn and were not present at Prestonpans.
John Campbell, 4th Earl of Loudoun and Sir John Cope had escaped by sea to London after the Battle of Prestonpans from whence Loudoun later returned north to Inverness to take command in the north but was forced with the Lord President Forbes and George Munro of Culcairn to withdraw through the Black Isle into Ross-shire being pressed by a much larger Jacobite force.
The commander of British forces, Prince William, Duke of Cumberland, had no wish to have the support of any Highland troops at the time for he distrusted them all and deliberately gave the Earl of Loudoun no help to extricate himself from his difficulties with the Jacobites in the north. Harry Munro was with George Mackay of Skibo, son of George Mackay, 3rd Lord Reay, at the Skirmish of Tongue in March 1746 where they defeated a Jacobite force and captured money and supplies that were meant for the Jacobite leader Charles Edward Stuart.
Three other companies of Loudoun's regiment raised in Argyll from the Clan Campbell came under the Duke of Cumberland's command in his march north from Stirling but they were used mainly as scouts and baggage guards. However, several of them, including one officer were killed when they fought at the Battle of Culloden. Loudon's Highlanders Regiment was at Culloden but Harry Munro himself was listed as absent "by HRH leave" presumably to try to deal with the problems at Foulis Castle which had been burned after the Battle of Falkirk.
At the request of Simon Fraser, 11th Lord Lovat, Harry Munro of Foulis and Ludovick Grant of Grant visited Lovat while he was imprisoned in the Tower of London having received the death sentence.
After the suppression of the rebellion, Loudon's Highlanders later took part in the mopping up operations based at Fort Augustus. The regiment remained in Scotland until May 1747 when they embarked at Bruntisland to join the allied army under Cumberland in Flanders.
The Munro company under Harry appears to have stayed in Scotland but in a letter from another officer in March 1748, Sir Harry is said to be going over to join the regiment. However, with the ending of the war in Flanders, Loudon's regiment was ordered back to Scotland and reduced at Perth in June of that year.