The exact dates of his birth and death are unknown. He was the second son of Richard Whalley, who had been High Sheriff of Nottinghamshire in 1595, by his second wife Frances Cromwell, an aunt of Oliver Cromwell. His great-grandfather was Richard Whalley (1499–1583), a prominent adherent of Edward Seymour, 1st Duke of Somerset, and a Member of Parliament. Edward Whalley is said to have started out as a woollen-draper. During the 1620s and 1630s, he was a farmer in Chadwell St Mary, Essex but this farming venture turned out not to be a success. In 1639, Whalley was forced to flee to Scotland to escape from his creditors leaving his wife behind him. On the outbreak of the English Civil War, he took up arms for Parliament and James Temple obtained a position for him as a cornet in the cavalry troop commanded by Temple’s cousin John Fiennes (the son of his uncle, Viscount Saye and Sele). He fought at the Battle of Edgehill and later became major of Cromwell's regiment of horse. He distinguished himself in the field and his conduct at Gainsborough in 1643 was especially praised by Cromwell. He fought at the Battle of Marston Moor, commanded one of Cromwell's two regiments of cavalry at the Battle of Naseby and at the capture of Bristol, was then sent into Oxfordshire, took Banbury, and was besieging Worcester when he was superseded, according to Richard Baxter, the chaplain of his regiment, because of his religious orthodoxy.