[2] He was a nephew of Sir Nicholas Throckmorton, one of Elizabeth's diplomats, who had held the post of Chief Justice of Chester but was removed in 1579, a year before his death.
In 1567, Throckmorton was betrothed to Anne Sutton, heir to the manors of Sedgely, Himley and Swinford in Staffordshire, and daughter of Sir Edward Sutton, 4th Baron Dudley and Katherine Brydges, who had been one of Queen Mary the I's Gentlewomen of the Privy Chamber, herself the daughter of John Brydges, 1st Baron Chandos, who was Lieutenant of the Tower of London during the reign of Mary I.
In Oxford he had come under the influence of Catholics, and when Edmund Campion and Robert Persons came to England in 1580 to conduct Jesuit propaganda, Francis was one of the members of the Temple who helped them.
[9] Following Throckmorton's return to England in 1583, he served as an intermediary for communications between supporters of the Catholic cause on the continent, the imprisoned Mary, Queen of Scots, and the Spanish ambassador Bernardino de Mendoza.
[13] Throckmorton's activities raised the suspicions of Sir Francis Walsingham, Elizabeth I's spymaster and he was arrested in October or in the first week of November in 1583.
He was convicted of high treason and executed by hanging at Tyburn on 10 July 1584, but on the scaffold he revoked his second confession, calling God to witness that it was drawn from him by the hope of pardon.
He confessed to writing a letter in cipher for Mary to send to the French ambassador Michel de Castelnau asking him to negotiate a pardon for Francis Throckmorton in a prisoner exchange.
Throckmorton's recruitment to act as a courier to Queen Mary and the way he was discovered by Walsingham's agents are depicted in Ken Follett's historical novel A Column of Fire.