A devout Puritan who fought for Parliament in the First English Civil War, Harley belonged to the moderate Presbyterian faction, which opposed the involvement of the New Model Army in the peace negotiations that followed victory in 1646.

Harley's refusal to support the Trial of Charles I led to his exclusion from the Long Parliament by Pride's Purge in December 1648, while his opposition to the king's execution in January 1649 meant he played little part in public affairs under the Commonwealth.

[2] The Harleys were one of the most powerful families in Herefordshire, while both Sir Robert and Lady Brilliana were Presbyterians who used their influence to appoint Nonconformist clergy to local positions.

[2] When the First English Civil War began in August 1642, the Harleys were among the minority of Herefordshire landed gentry who supported Parliament, and the county became a major source of Royalist recruits.

[6] However, an attack on Gloucester itself was successfully repulsed, and in August Harley was made colonel of a new infantry regiment raised as part of Massey's Army of the Western Association.

[2] This was repulsed, and with Prince Rupert taking many Royalist troops north for the Marston Moor campaign, Parliamentarian forces were able to capture Monmouth in September.

[9] When the New Model Army was formed in April 1645, Harley was given command of one of its twelve authorised infantry regiments; the previous colonel, Harry Barclay, and his deputy John Innes, were Scottish professional soldiers who resigned under orders from the Covenanter government.

He missed Naseby after being wounded in another skirmish outside Ledbury in April 1645, and was appointed Governor of Canon Frome in August, which meant he did not participate in the New Model's Western Campaign.

Regional forces like Massey's Western Association continued to exist independently of the New Model, and in January 1646 Harley was appointed Commander of Horse for Herefordshire and Radnorshire.

[13] However, victory resulted in increasingly bitter disputes over the post-war political settlement between radicals within the New Model like Oliver Cromwell, and Parliamentary moderates, the most prominent being Denzil Holles.

Seeking to ensure his own troops were retained and to re-assert his position in local politics, Harley became involved in a power struggle with the other prominent Parliamentarian in the region, Colonel John Birch, Governor of Hereford.

[17] He retained considerable influence in Herefordshire, and despite being arrested during the unsuccessful Monmouth Rebellion in June 1685, James II made several efforts to attract his backing, all of which he refused.

[17] He returned to Parliament in February 1693 as a Country Whig, often voting with the Tories; his opposition to the government was largely due to concerns over the expansion of the standing army for the Nine Years War.