His great-grandfather was Richard Whalley (1499–1583), a prominent adherent of Edward Seymour, 1st Duke of Somerset, and a Member of Parliament.

He was chosen to be a Commissioner (judge) at the trial of Charles I and was the fourth to sign the king's death-warrant, immediately after Cromwell.

[4] Whalley took part in Cromwell's Scottish Expedition, was wounded at the Battle of Dunbar, and in the autumn of 1650, was active in dealing with the situation in the north.

He supported the "Petition and Advice," except as regards the proposed assumption of the royal title by Oliver Cromwell, and became a member of the newly constituted House of Lords in December 1657.

[3][4] At the Restoration, Whalley, with his son-in-law, Major-General William Goffe, escaped to North America, and landed at Boston on 27 July 1660, where they were well received by Governor John Endecott and visited by the principal persons of the town.

[7] The two moved to New Haven, Connecticut, where John Dixwell, also condemned as a regicide, was living under the assumed name of James Davids.

They again lodged secretly with Davenport and a number of other sympathizers until 13 May, when they resorted to hiding in some woodland and a cave on Providence Hill (spending some nights in a nearby house).

On 13 October, travelling only by night, they set off for Hadley, about one hundred miles away to the north in western Massachusetts, where the minister, John Russell, had arranged for them to live with him.

In the first few years, they were in constant fear of discovery and were much relieved to read in the newspapers that they were thought to have died in Switzerland while living in exile with other regicides.

Hadley also has two parallel streets named after Goffe and Whalley, as well as a memorial stone at the former site of John Russell's home.

Whalley and Goffe appear as the protagonists of British author Robert Harris’s 2022 novel Act of Oblivion, which depicts their flight across New England.