Glencairn, Maxwell, and other Scottish peers, who professed to desire the marriage of the young Queen Mary to Prince Edward, afforded Wharton active employment for the rest of Henry VIII's reign. With the accession of Edward VI a great effort was made by Somerset to complete the marriage between Mary and the young king, and a pretext for his invasion was afforded by a Scottish raid in March 1546–7. On the 24th the council asked Wharton for two despatches, one giving an exact account of the raid, the other magnifying the number of raiders and towns pillaged. The latter was intended to justify English reprisals in the eyes of the French king and prevent his giving aid to the Scots (Acts P. C. 1547–50, p. 461; Selve, Corr. Pol. p. 124). In September following, while Somerset invaded Scotland from Berwick, Wharton and the Earl of Lennox created a diversion by an incursion on the west. They left Carlisle on the 9th, with two thousand foot and five hundred horse, and on the 10th captured Milk Castle; on the following day Annan, and on the 12th Dronok, surrendered, but on the 14th they returned to Carlisle, explaining their lack of further success by want of victual and ordnance. Wharton was excused attendance at the ensuing session of parliament, his presence being needed on the borders.
In the autumn William, thirteenth baron Grey de Wilton [q. v.], was appointed warden of the east marches, but his relations with Wharton were strained, and led eventually to a challenge from Henry Wharton to Grey, though Somerset on 6 Oct. 1549 forbade a duel. This want of harmony probably contributed to the failure of their joint invasion of Scotland in February 1547–8. Wharton and Lennox left Carlisle on the 20th, sending on Henry Wharton to burn Drumlanrig and Durisdeer. Wharton himself occupied Dumfries and Lochmaben, but on the 23rd a body of ‘assured’ Scots under Maxwell, who accompanied Henry Wharton, changed sides, joined Angus, and compelled Henry Wharton, with his cavalry, to escape across the mountains. News was brought to Carlisle that the whole expedition had perished, and Grey, who had penetrated as far as Haddington, retreated. In reality the Scots, after their defeat of Henry Wharton, were themselves repulsed by his father; many were captured or killed, but Wharton was forced to retreat, and Dumfries again fell into Scottish hands. In revenge for Maxwell's treason, Wharton hanged his pledges at Carlisle, and thus initiated a lasting feud between the Whartons and the Maxwells.
After Somerset's fall in October 1549 Wharton's place as warden was taken by his rival, Lord Dacre; but early in 1550 Wharton was appointed a commissioner to arrange terms of peace with Scotland and afterwards to divide the debatable land; he was one of the peers who tried and condemned Somerset on 1 Dec. 1551. On 8 March 1551–2 the council effected a reconciliation between Wharton and Dacre; and when, in the following summer, Northumberland secured his own appointment as lord-warden-general, Wharton was on 31 July nominated his deputy-warden of the three marches (Royal MS. 18 C. xxiv. f. 246 b). On Edward VI's death Dacre sided at once with Mary, and it was reported that Wharton was arming against him. If Wharton ever had this intention he quickly abandoned it, and Mary, affecting at least to disbelieve the accusations against him, continued him in the office of warden, while his eldest son became one of the queen's trusted confidants. Dacre was, however, appointed warden of the west marches, Wharton continuing in the east and middle marches, and residing mainly at Alnwick. Wharton's own sympathies were conservative in religious matters; he had voted against the act of 1548–9 enabling priests to marry, against that of 1549 for the destruction of the old service books, and against the second act of uniformity in 1552, though he had acted as chantry commissioner under the dissolution act of 1547 (Leach, English Schools at the Reformation, ii. 185).
In spite of advancing years, Wharton retained his wardenry throughout Mary's reign, the Earl of Northumberland being joined with him on 1 Aug. 1557 when fresh trouble with the Scots was imminent owing to the war with France. In the parliament of January 1557–8 a bill was introduced into the House of Lords for punishing the behaviour of the Earl of Cumberland's servants and tenants towards Wharton, but it did not get beyond the first reading. In June 1560 Norfolk, then lieutenant-general of the north, strongly urged Wharton's appointment as captain of Berwick, as likely to ‘prevent all misfortunes that might fall,’ his restoration to the west marches being impossible because of his feud with Maxwell, who was now friendly to the English (Hatfield MSS. i. 200, 229). The recommendation was apparently not adopted, either because of Wharton's age, or because he was rendered suspect by his son's conduct. He saw no further service, died at Helaugh on 23 or 24 Aug. 1568, and was buried there on 22 Sept. His will was
