On Tuesday, 11 April 1447, Cardinal Beaufort died at Winchester. Henry, it is evident, received private news of the event on the same day, and immediately wrote to the monks recommending Waynflete for election to the bishopric (ib. p. 299). On Wednesday, 12 April, the official letter announcing the vacancy and praying license to proceed to election was despatched to the king. Letters patent were issued, dated Canterbury, 11 April, granting Waynflete custody of the temporalities of the see (Pat. Roll. 25 Henry VI, pt. 2, m. 30). On 14 April he made his first presentation. The congé d'élire under the privy seal is dated 15 April at Canterbury (Rymer, Fœdera, xi. 153). On Monday, 17 April, the prior and chapter made a formal return of the election. The papal bull nominating Waynflete bishop bears the early date of 10 May. On 3 June Waynflete took the oath of fealty to the king in person (Le Neve, Fasti, iii. 15). On 4 June the temporalities were formally restored (Fœdera, xi. 172). On 16 June Waynflete made profession of canonical obedience at Lambeth. He was consecrated at Eton on 13 July; on 18 July he received the spiritualities. He held his first general ordination on Sunday, 23 Dec. following, at Eton, by special license of the bishop of Lincoln. On 19 Jan. 1448 he was enthroned at Winchester in presence of the king. Henry's choice was clearly a personal preference. As John Capgrave, the contemporary chronicler, dryly remarks, Waynflete ‘carus, ut putatur, domino regi habetur, non tam propter scientiam salutarem quam vitam cœlibem.’ Henry himself, in assigning to Waynflete a paramount place among the executors of his will (12 March 1448), expresses his attachment to him (Chandler, p. 318).
Little more than a year after his advancement Waynflete obtained letters patent, dated 6 May 1448, for the foundation of a hall dedicated to St. Mary Magdalen in the university of Oxford. Its charter was dated 20 Aug. 1448 (Wood, Ant. pp. 307–8; Chandler, p. 330). Its object was the study of theology and philosophy.
The rebellion of Jack Cade [see Cade, John] at Whitsuntide 1450 first brought Waynflete into contact with the turbulent politics of the period. On the morning of Monday, 6 July, Cade having retreated into Southwark, an armistice was proclaimed. Waynflete, who ‘for some safeguard laie then at Haliwell’ (Holinshed, Chron. iii. 226), the priory in Shoreditch (Maitland, Hist. of London, ed. 1772, ii. 1368), and not at his Southwark palace, received a summons to attend a council in the Tower. Thence Waynflete, with other lords (Wyrcestre's Chron. p. 768), proceeded to treat with Cade in the church of St. Margaret, Southwark, within his own diocese. He received Cade's list of grievances, and promised both a general pardon under the great seal and a special one to Cade himself. The insurgents then dispersed from Southwark. But on 1 Aug. 1450 a special commission was issued into Kent to try those who, after the proclamation of pardon, had remained in arms at Deptford and Rochester. The commission included Waynflete's name (Pat. Rolls, 28 Henry VI, pt. ii. m. 17). Many executions followed.
Behind Cade's rebellion lay the sympathies of the Yorkists, and there are signs that Waynflete's intervention ultimately involved him in formidable odium. In September 1450 disturbances broke out at Winchester, the citizens refusing their customary dues at St. Giles' fair (Hist. MSS. Comm. App. to 6th Rep. p. 603). It is possible that the despatch of a quarter of one of Cade's adherents for exhibition in that city had provoked irritation (Proceedings of the Privy Council, vi. 108). The citizens of Winchester submitted, and were pardoned. But a more serious attack threatened. On 7 May 1451 Waynflete executed a remarkable document, appealing for protection to the pope and the archbishop of Canterbury. The recitals show that some attempt was on foot to deprive him of his see by a process in the spiritual courts (Registr. Waynflete, i. 2, f. 11; Chandler, pp. 66–7).
At this time Henry VI was relying much on Waynflete's counsels. They were together at Canterbury in August 1451. In September the bishop issued from St. Albans a commission for the visitation of his diocese, alleging ‘arduous and unexpected business concerning the king and the realm’ (Chandler, p. 69). Upon the approach to London of Richard, duke of York, with an army in March 1452, Henry despatched Waynflete to make terms.
In July 1453 Henry VI became totally paralysed. His son Edward, prince of Wales, was born on 13 Oct., and baptised by Waynflete on the following day (Engl. Chron., p. 193). On 23 March 1454 Waynflete, with a committee of lords, endeavoured to procure from the king an authorisation for the conduct of the government by Richard, duke of York, to whose inevitable ascendancy he seems to have resigned himself. He reported to the House of Lords that the imbecility of the king rendered the errand fruitless. During this interregnum he was constant in his attendances at the council,