On 6 February 1532 he was made Justice of the Peace for the East Riding of Yorkshire, and on 19 March for Northumberland, and he was usually included in the commissions for Cumberland and Westmorland.
His appointment as Warden of the West Marches was suggested as a reward for his services; but Norfolk instead recommended Henry Clifford, 1st Earl of Cumberland, for the post.
He was unpopular with the older nobility, being one of the new men on whom the Tudors relied; Robert Holgate, as President of the Council of the North, commented on the disdain of his neighbours.
[3] During 1542 both English and Scots were preparing for war, and Wharton submitted a plan for raiding Scotland and seizing the person of James V at Lochmaben; the council, however, disapproved of the idea.
At supper on the 23rd he received definite information of an impending attack on the morrow: the Scots were said to be fourteen (or even twenty) thousand strong, while Wharton could only muster a few hundred men.
[3] Before the Privy Council had heard of his victory at Solway Moss, on 30 November they wrote requesting Wharton to review the building works of the Moravian military engineer Stefan von Haschenperg at Carlisle.
She came to him at Carlisle Castle in February 1543, at the start of the war known as the Rough Wooing and said that the Laird of Buccleuch was willing to capture Mary, Queen of Scots and bring her to him.
Later in May 1544 border troops were sent to accompany Henry VIII to France, but Wharton was refused leave to join them on the grounds that he could not be spared from the marches.
[9] Border forays and intrigues with Angus, Glencairn, Lord Maxwell, and others, who professed to desire the marriage of the Mary Queen of Scots to Edward, occupied Wharton for the rest of Henry VIII's reign.
[10] With the accession of Edward VI the War of the Rough Wooing continued, with effort being made by Somerset as Lord Protector to complete the marriage, and a Scottish raid in March 1547 provided a pretext for his invasion.
On the 24th the council asked Wharton for two despatches, one giving an exact account of the raid, the other exaggerating the number of raiders and towns pillaged.
In September following, while Somerset invaded Scotland from Berwick-upon-Tweed, Wharton and the Earl of Lennox created a diversion by an incursion on the west.
[3] In spite of advancing years, Wharton retained his wardenry throughout Mary's reign, the Earl of Northumberland being joined with him on 1 August 1557 when fresh trouble with the Scots was imminent (owing to the war with France).
In the parliament of January 1558 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.
[3] In June 1560 Norfolk, then lieutenant-general of the north, strongly urged Wharton's appointment as captain of Berwick-upon-Tweed, his restoration to the west marches being impossible because of his feud with Maxwell, who was now friendly to the English; but the recommendation was not adopted.