Sir Francis Windebank (1582 – 1 September 1646) was an English politician who was Secretary of State under Charles I.
Francis was the only son of Sir Thomas Windebank of Hougham, Lincolnshire, who owed his advancement to the Cecil family, Francis entered St John's College, Oxford, in 1599, coming there under the influence of the Archbishop of Canterbury, William Laud. After a few years of continental travel (1605–1608), he settled at Haines Hill at Hurst in Berkshire and was employed for many years in minor public offices, eventually becoming clerk of the council.
In June 1632, he was appointed by King Charles I as Secretary of State in succession to Lord Dorchester, his senior colleague being Sir John Coke, and he was knighted. His appointment was mainly due to his Spanish and Roman Catholic sympathies. The first Earl of Portland, Francis, Lord Cottington, and Windebank formed an inner group in the council, and with their aid the king carried on various secret negotiations, especially with Spain.
In December 1634 Windebank was appointed to discuss with the papal agent Gregorio Panzani the possibility of a union between the Anglican and Roman Churches, and expressed the opinion that the Puritan opposition might be crippled by sending their leaders to the war in the Netherlands.
Windebank's efforts as treasury commissioner in 1635 to shield some of those guilty of corruption led to a breach with Archbishop Laud. In the same year Windebank was one of the promoters of the Courteen association. and the next year he was for a time disgraced for issuing an order for the conveyance of Spanish money to pay the Spanish troops in the Netherlands.