He was the son of Richard Harper of Latton, Harlow, Essex and his wife Constance, the daughter of Sir Robert Chamberlain of Capel and Gedding, Suffolk.
By June 1556, Harper had married again, to Audrey Gainsford, widow of George Taylor of Lingfield, Surrey, and daughter of Sir John Gainsford (d.1540) of Crowhurst, Surrey, by his fifth wife, Audrey Shaa, daughter of Sir John Shaa, Lord Mayor of London.
In 1540, the King married Catherine Howard, whose mother was Joyce Culpeper, a distant relative of Harper's stepfather.
Expecting a French invasion, Harper was involved in improving the defences of Kent, the English county nearest France.
He had some association with John Dudley, 1st Duke of Northumberland, and when Mary I of England reclaimed the throne from Jane Grey, she ordered him to come to court and be given a general pardon for any treason he may have been involved in.
The next year there was widespread discontent at the Queen's marriage to Philip II of Spain, and Harper joined the rebellion led by Thomas Wyatt the younger.
He changed sides several times and was eventually imprisoned in the Tower of London, but pardoned without trial on 6 November 1555.
After her death his lands were inherited by his sister's son-in-law, William Isley, husband of Ursula Clifford.