Born at Kirkcaldy about 1512, he was educated at the University of St Andrews and on the continent, where he adopted Protestant views. Returning to Scotland, he continued his legal studies and in 1538 was appointed a lord of session. He married Christian Scheves, and in 1539 was granted the estate of Halhill in Fife, after which lie is generally named. Before 1540 he was sworn of James V of Scotland's privy council, and was known as one of the party in favour of the English alliance and of an ecclesiastical reformation. He is also described as treasurer to James, but the regent Arran appointed him secretary in the new government of the infant Queen Mary (January 1543).
He promoted the act permitting the reading of the Scriptures in the vulgar tongue, and was one of the commissioners appointed to arrange a marriage treaty between the little queen. and the future Edward VI In London he was not considered so complaisant as some of the other commissioners, and was not made privy to all the engagements taken by his colleagues. But Beton "loved him worst of all," and, when Arran went over to the priestly party, Balnaves was, in November 1543, deprived of his offices and imprisoned in Blackness Castle.
He was released by the arrival of Hertford's fleet in the following May, and from this time he became a paid agent of the English cause in Scotland. He took no part in the murder of Beton, but was one of the most active defenders of the castle of St. Andrews. He was made English paymaster of the forces in St. Andrews. When that castle surrendered to the French in July Balnaves was taken prisoner to Rouen.
Somerset made vain efforts to procure his release and continued his pension. He made himself useful by giving information to the English government, and even Mary Tudor sent him a reward in June 1554. Balnaves also busied himself in writing what Knox calls "a comfortable treatise of justification," which was found in manuscript with a preface by Knox, among the reformer's papers, and was published at Edinburgh in 1584 under the title The Confession of Faith.
In 1557 Balnaves was permitted to return to Scotland and regain his property; probably it was thought that Mary Tudor's burnings would have cooled the ardour of his English affections, and that in the war threatening between two Catholic countries, Balnaves would serve his own. The accession of Queen Elizabeth I changed the situation, and Mary of Guise had reasons for accusing him of "practices out of England". He took, in fact, an active part in the rising of 1559 and was commissioned by the Congregation to solicit the help of the English government through Sir Ralph Sadleir at Berwick.
He was also selected one of the Scots representatives to negotiate with the Duke of Norfolk in February 1560. In 1563 he was restored to his office as lord of session, and was one of those appointed by, the General Assembly to revise the Book of Discipline. He was one of Bothwell's judges for the murder of Darnley in 1567, and in 1568 he accompanied Moray to the York inquiry into Queen Mary's guilt.
He resigned his judicial office in 1574, and died in 1579 at Edinburgh. He has been claimed as a Scots bard on the strength of one ballad, "O gallandis all, I cry and call," which is printed in Allan Ramsay's Evergreen (2 vols. 1724-1727).