His distant cousin Ceadagh O'Farrell was killed at the Battle of the Boyne in 1690 fighting for the Jacobites, while other relatives joined the French Irish Brigade, so Francis was unusual in serving the Protestant William of Orange.

By 1688, he had reached the rank of Lieutenant Colonel and was part of the invasion force that accompanied William of Orange to England in the November 1688 Glorious Revolution.

On 1 March 1689, O'Farrell was commissioned Colonel of the Earl of Mars Regiment in place of Thomas Buchan, a Scottish Catholic who had remained loyal to James.

It reached Flanders in time to fight at the Battle of Walcourt in August 1689 and is listed in the 1691 return as a "Fusilier" regiment, a designation reserved for elite units.

[4] William dealt harshly with the officers from Deinze and Diksmuide; Ellenberg was executed in Ghent on 30 November, O'Farrell dismissed and those who signed the surrender documents court-martialled.