In 1631, after he had been ordained and had acted for some years as regent in the university, he was appointed to the living of Kilwinning in Ayrshire. In 1638 he was a member of the famous Glasgow Assembly, and soon after he accompanied Leslie and the Scottish army as chaplain or preacher. In 1642 he was made professor of divinity at Glasgow, and in the following year was selected as one of the five Scottish clergymen who were sent to the Westminster Assembly.
In 1649 he was one of the commissioners sent to Holland for the purpose of inviting Charles II to Scotland, and of settling the terms of his admission to the government. He continued to take an active part in all the minor disputes of the church, and in 1661 was made principal of Glasgow University. He died in August of the following year, his death being probably hastened by his mortification at the apparently firm establishment of episcopacy in Scotland. Baillie was a man of learning and ability; his views were not extreme, and he played but a secondary part in the stirring events of the time. His Letters, by which he is now chiefly remembered, are of first-rate historical importance, and give a very lively picture of the period.
A complete memoir and a full notice of all his writings will be found in D. Laing's edition of the Letters and Journals of Robert Baillie (1637-1662), Bannatyne Club, 3 vols. (Edinburgh, 1841-1842). Among his works are Ladensium autokatakrisis, an answer to Lysimachus Nicanor, an attack on Laud and his system, in reply to a publication which charged the Covenanters with Jesuitry; Anabaptism, the true Fountain of Independency, Brownisme, Antinomy, Familisme, etc., a sermon; An Historical Vindication of the Government of the Church of Scotland; The Life of William (Laud) now Lord Archbishop of Canterbury Examined (London, 1643); A Parallel of the Liturgy with the Mass Book, the Breviary, the Ceremonial and other Romish Rituals (London, 1661).