Balfour seems to have afterwards joined in the proceedings of the Reformers, but only with courtier-like temperance, and without exhibiting much zeal in the Protestant cause. He was preferred to the ecclesiastical appointment of official of Lothian, and afterwards became rector of Flisk, a parish in his native county. In 1563, he was appointed by Queen Mary to be a Lord of Session, the court then being composed partly of churchmen, and partly of laics. In 1564, when the Commissary court was instituted in place of the ecclesiastical tribunal, which had been dissolved at the Reformation, Balfour became one of the four commissaries, with a salary of four hundred merks, while the others had only three hundred. In July, 1565, the Queen extended the further favour of admitting him into her privy council.
Balfour was one of those servants of the state, who, being advanced rather on account of merit than birth, used at all times to give great offence to the Scottish nobility. It seems to have never been supposed by this haughty class, that there was the least necessity for ingenious or faithful service in the officials employed by majesty; birth and following were the only qualifications allowed by them to be of any value. Accordingly, it is not surprising to find that the same conspiracy which overthrew the "kinless" adventurer Rizzio, contemplated the destruction of Balfour. He was so fortunate, however, as to escape, and even derived some advantage from the event, being promoted to the office of clerk-register, in room of Mr James Macgill, who was concerned in the conspiracy. He was also about this time made a knight, and appointed to be one of the commissioners for revising, correcting, and publishing the ancient laws and statutes of the kingdom.
In the beginning of the year 1567, Sir James Balfour was appointed governor of Edinburgh castle. In this important situation, he naturally became an object of great solicitude to the confederate lords, who, in the ensuing May, commenced a successful rebellion against Queen Mary. It would appear that Sir James was not now more loyal than many other persons who had experienced the favour of Mary. He is said to have even been the means of throwing into the hands of the confederates that celebrated box of letters, upon which they endeavoured to ground the proof of her guilt. There can be no doubt that he was at this time in the way of receiving high favours from the Earl of Murray, who was the chief man opposed to the dethroned queen. He was, in September, 1567, admitted by Murray a lord of his privy council, and made commendator of the priory of Pittenweem; and in December, a bargain was accomplished, by which he agreed to accept a pension of L.500 and the presidency of the Court of Session, in lieu of the clerk-registry, which Murray wished to be restored to his friend Macgill. Sir James continued faithful to the party which opposed Queen Mary, till the death of Murray, January, 1569-70, when he was in some measure compelled to revert to the Queen's side, on account of a charge preferred against him by the succeeding Regent, Lennox, who taxed him with a share in the murder of Darnley. For this accusation no proof was ever adduced, but
tude of mind remained unsubdued, and he comforted his fellow-prisoners with hopes of release. To their anxious desponding inquiries, natural to men in their situation, 'If he thought they would ever obtain their liberty,' his uniform answer was, 'God will deliver us to his glory, even in this life.' While they lay on the coast between Dundee and St Andrews, Mr (afterwards Sir) James Balfour, who was confined in the same ship, desired him to look at the land and see if he knew it. Though at that time very sick, he replied, 'Yes; I know it well, for I see the steeple of that place where God first opened my mouth in public to his glory: and I am fully persuaded, how weak soever I now appear, that I shall not depart this life till that my tongue shall glorify his godly name in the same place.' This striking reply Sir James repeated in the presence of many witnesses, a number of years before Knox returned to Scotland, and when there was very little prospect of his words being verified." Life of Knox, 1st edit. p. 53.
