He was present at the battle of Edgehill in October 1642, after which, while hastening to Oxford to prepare for the king's visit to Christ Church, he was captured by a troop of Lord Say's soldiers from Broughton House, being soon afterwards set free on the surrender of the place to the king's forces.
It has also been shown by Broughton that C. Peruviana, which yields cinchonine but no quinine at a height of 6000 ft., when grown at 7800 ft.
Warburton now received from Sir Robert Sutton the small living of Greasley, in Nottinghamshire, exchanged next year for that of Brant Broughton, Lincolnshire.
At Brant Broughton for eighteen years he spent his time in study, the first result of which was his treatise on the Alliance between Church and State (1736).
He now showed that he had not by his charities wronged his relations by settling on his greatnephew and heir Thomas Wykeham, whom he had educated at Winchester and New College, Broughton Castle and estates, still held by his descendants in the female line, the family of Twisleton-Wykeham-Fiennes (peerage of Saye and Sele).