Scottish professional soldier who commanded a regiment under Gustavus Adolphus in Sweden before returning to Scotland in 1639 to fight for the Covenanters in the Bishops War.In 1644, Baillie marched into England with the Army of the Covenant. He commanded the Scottish infantry on the Allied right wing at the battle of Marston Moor where his pikemen held firm against the Royalist cavalry. In 1645, he commanded the detachment sent from Lord Leven's army against the Marquis of Montrose. On his arrival in Scotland, Baillie successfully manoeuvred to prevent Montrose from marching south. In April, he almost caught up with Montrose at Dundee but Montrose succeeded in escaping into the Highlands. Baillie then split his forces, planning to trap Montrose between his own troops and a detachment commanded by Sir John Hurry. However, Montrose decisively defeated Hurry at Auldearn in May 1645; two months later he defeated Baillie himself at Alford, where almost the entire Covenanter army was slaughtered. The heavy butchery of covenating troops at these encounters hardened hearts and were a prelude to the fate the Irish would receive in turn. After these disasters, Baillie tendered his resignation. This was rejected by the Estates. Instead a new army was raised. Baillie retained command but was now accompanied by a Committee of War headed by the Marquis of Argyll. Against Baillie's advice, a battle with Montrose was forced at and decisively lost at Kilsyth, Montroses last victory.

During the Second Civil War, Baillie commanded the infantry in the Duke of Hamilton's ill-fated Engager invasion of England. The Engagers were defeated by Cromwell in the three-day battle of Preston in August 1648. When Hamilton escaped, Baillie was ordered to surrender the infantry. In despair, he pleaded with his fellow officers to end his disgrace by shooting him, but no-one obliged.