The 4th Baron died on 9 August 1396, and Willoughby inherited the title as 5th Baron, and was given seisin of his lands on 27 September. Hicks notes that the Willoughby family had a tradition of military service, but that the 5th Baron 'lived during an intermission in foreign war and served principally against the Welsh and northern rebels of Henry IV'. Willoughby joined Bolingbroke, the future King Henry IV, soon after his landing at Ravenspur, was present at the abdication of Richard II in the Tower on 29 September 1399, and was one of the peers who consented to King Richard's imprisonment. In the following year he is said to have taken part in Henry IV's expedition to Scotland. In 1401 he was admitted to the Order of the Garter, and on 13 October 1402 was among those appointed to negotiate with the Welsh rebel, Owain Glyndŵr. When Henry IV's former allies, the Percys, rebelled in 1403, Willoughby remained loyal to the King, and in July of that year was granted lands that had been in the custody of Henry Percy, who was killed at the Battle of Shrewsbury on 21 July 1403. Willoughby was appointed to the King's council in March 1404. On 21 February 1404 he was among the commissioners appointed to expel aliens from England. In 1405 Hotspur's father, Henry Percy, 1st Earl of Northumberland, again took up arms against the King, joined by Lord Bardolf, and on 27 May Archbishop Scrope, perhaps in conjunction with Northumberland's rebellion, assembled a force of some 8000 men on Shipton Moor. Scrope was tricked into disbanding his army on 29 May, and he and his allies were arrested. Henry IV denied them trial by their peers, and Willoughby was among the commissioners who sat in judgment on Scrope in his own hall at his manor of Bishopthorpe, some three miles south of York. The Chief Justice, Sir William Gascoigne, refused to participate in such irregular proceedings and to pronounce judgment on a prelate, and it was thus left to the lawyer Sir William Fulthorpe to condemn Scrope to death for treason. Scrope was beheaded under the walls of York before a great crowd on 8 June 1405, 'the first English prelate to suffer judicial execution'. On 12 July 1405 Willoughby was granted lands forfeited by the rebel Earl of Northumberland. In 1406 Willoughby was again appointed to the Council. On 7 June and 22 December of that year he was among the lords who sealed the settlement of the crown.
*Robert Willoughby, 6th Baron Willoughby de Eresby, who married firstly, Elizabeth Montagu, and secondly, Maud Stanhope.
*Sir Thomas Willoughby, who married Joan Arundel, daughter and co-heiress of Sir Richard Arundel by his wife, Alice. Their descendants, who include Catherine Willoughby, Duchess of Suffolk, inherited the Barony. Catherine became the 12th Baroness and the title descended through her children by her second husband, Richard Bertie.
Willoughby died at Edgefield, Norfolk on 4 December 1409 and was buried in the Church of St James in Spilsby, Lincolnshire, with his first wife. A chapel in the church at Spilsby still contains the monuments and brasses of several early members of the Willoughby family, including the 5th Baron and his first wife.
