Blakiston was the son of Marmaduke Blakiston, a prebendary of Durham. He became a prosperous mercer in Newcastle, and its MP in 1641. Unlike his father, he was a staunch Puritan and in 1636 was cited before the High Commission Court for nonconformity and defaming the vicar of Newcastle. He was fined 100 pounds and excommunicated. After the Scots army stormed Newcastle in 1644, Blakiston became mayor in place of Sir John Marley. Blakiston was one of Charle I's judges and signed the king's death warrant.