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 1613. His great-great-grandfather, Sir William Willoughby of Parham, was nephew of William Willoughby, ninth baron Willoughby de Eresby, whose daughter Katharine, duchess of Suffolk, married as her second husband Richard Bertie, and was mother of Peregrine Bertie, eleventh baron Willoughby de Eresby [q. v.] Sir William was created first baron Willoughby of Parham in Suffolk on 20 Feb. 1546–7, and died in August 1574. His son Charles, second baron, is frequently confused (e.g. in indexes to Cal. State Papers, Dom., Cal. Hatfield MSS., and Leycester Correspondence) with his cousin, Peregrine Bertie; he was grandfather of William, third baron Willoughby of Parham, who died on 28 Aug. 1617, and was succeeded by his eldest son Henry. Henry died about 1618, when little more than five years old, and the title passed to his younger brother, Francis (, Peerage, ed. Brydges, vi. 613).

In 1636 Francis Willoughby complained of partiality in the levying of ship-money in Lincolnshire; in 1639 he answered with a great lack of zeal the king's summons to serve against the Scots; in the summer of 1640 his name was attached to some copies of the petition of the twelve peers to the king which led to the calling of the Long parliament. Though not at all conspicuous among the opposition, it is evident he was disaffected to the government (Cal. State Papers, Dom. 1636–7, 1638–9 p. 435, 1640 p. 641). When the breach between the king and the parliament widened, Willoughby was appointed by the latter lord-lieutenant of the district of Lindsey in Lincolnshire, and, in defiance of the king's direct orders, put into execution the militia ordinance (Lords' Journals, iv. 587, v. 115, 127, 155). He was given command of a regiment of horse under the Earl of Essex, but arrived too late to take part in the battle of Edgehill (, Army Lists, p. 48;, Memorials, i. 187). On 9 Jan. 1643 he was made, by a special ordinance, lord-lieutenant and commander-in-chief in Lincolnshire ({{sc|Husband}, Ordinances, 1643, p. 834). On 16 July 1643 he surprised Gainsborough and took prisoner the Earl of Kingston, but was immediately besieged there by the royalists. Cromwell and Sir John Meldrum [q. v.] defeated the besiegers (28 July) and threw some powder into the town, but Willoughby was obliged to surrender on 30 July (Mercurius Aulicus, 27 July–3 Aug. 1643; Life of Col. Hutchinson, i. 217, 223;, Cromwell, letters xii. xiv.). A few days later he was forced to abandon Lincoln also, and to retire to Boston, which he expected to be unable to hold. ‘Without we be masters of the field,’ he wrote to Cromwell, ‘we shall be pulled out by the ears one after another’ (cf. Transactions of the Royal Historical Society, 1899, p. 53). Lincolnshire was added to the eastern association on 20 Sept. 1643, and recovered by Manchester's victory at Winceby on 11 Oct. Willoughby joined Manchester just before the battle, and captured Bolingbroke Castle in Lincolnshire on 14 Nov. 1643 (, God's Ark, pp. 44, 67). In March 1644 he took part in Sir John Meldrum's abortive attempt to capture Newark, and the ill success of the siege was freely attributed to the refusal of Willoughby's men to obey Meldrum (A Brief Relation of the Siege of Newark, 1643, 4to).

Willoughby's military career closed in a series of quarrels. On 22 Jan. 1644 Cromwell complained to the House of Commons of the license which Willoughby tolerated among his troops (, Studies and Illustrations of the Great Rebellion, p. 580; Mercurius Aulicus, 2 April 1644). Angry at this, and at his supersession by Manchester, Willoughby sent Manchester a challenge, for which, as a breach of privilege, he was obliged to ask the pardon of the House of Lords (Lords' Journals, vi. 405, 409, 413). He succeeded in getting Lieutenant-colonel Bury censured and Colonel Edward King committed to Newgate for their criticisms of his conduct as a general; but King was released by order of the House of Commons (ib. vi. 528, 531, 557, 571–6, 595, 600, 605, 612). In consequence of these personal slights he became bitterly dissatisfied. ‘We are all hasting to an early ruin,’ was his view of public affairs in 1644. ‘Nobility and gentry are going down apace’ (Hist. MSS. Comm. 4th Rep. p. 268;, ii. 366). In December 1645 parliament voted that the king should be asked to make Willoughby an earl, and employed him as one of its commissioners to the Scottish army (, i. 541, 548). Clarendon describes him as of great esteem among the presbyterians, ‘though not tainted with their principles’ (Rebellion, xi. 35). In 1647 he was one of the leaders of that party in parliament, and on 30 July 1647, after the secession of the independent members of the two houses, he was elected speaker of the lords in place of Manchester (, vi. 652). When the independents and the army triumphed, he was one of the seven lords impeached on 8 Sept. 1647, and remained for four months in prison. On 19 Jan. 1648 the lords released the accused peers on the ground that no charge had been presented against them. Articles of impeachment were sent up to the House of