Sir Christopher was brother of the poet, John Milton, being the younger son of John Milton, scrivener, by Sarah Jeffrey, his wife. He was born in Bread Street, London in November 1615 and educated at St. Paul's School and Christ's College, Cambridge, where he was admitted as a pensioner on 15th February 1631. Later that year, he entered the Inner Temple where, having left the university without a degree, he was called to the bar in 1639.

At the outbreak of the Civil War, Christopher was residing in Reading, in Berkshire, and, by virtue of a commission under the Great Seal, sequestered the estates of parliamentarians in three counties. After the surrender of Reading to Parliament in April 1643, he "steered his course according to the motion of the King’s army," and was in Exeter during Fairfax's siege of that place. Upon its surrender, in the Spring of 1646, his town house, the ‘Cross Keys’ in Ludgate, was sequestered, and he compounded for £80, a tenth of its value. Only a moiety of the composition, however, was paid by him and enquiries, apparently ineffectual, were made for estates supposed to belong to him in Suffolk and Berkshire. During the Commonwealth, his legal practice consisted chiefly of composition cases, among them that of his brother’s mother-in-law, Mrs. Anne Powell.

In November 1660, Christopher was elected a bencher of the Inner Temple, where he was Reader in the Autumn of 1667. At the time of his brother’s death, whose nuncupative will he attested on 5th December 1674, he was Deputy-Recorder of Ipswich. In later life, he was, or professed to be, a Roman Catholic and, though no great lawyer, was accordingly invested with the coif, knighted and raised to the Exchequer Bench by his fellow catholic, King James II, in late April 1686. His tenure of office was equally undistinguished and brief. On 16th April 1687, he was transferred to the Court of the Common Pleas, being dispensed from taking the oaths, and, on 6th July 1688, he was discharged as super­annuated, though retaining his salary.

Sir Christopher died in March 1693, and was buried, on 22nd of that month, in the church of St. Nicholas in Ipswich. Besides his house in Ipswich, he had a villa at Rushmere, about two miles from the town. He married, probably in 1638, Thomasine, daughter of William Webber of London, by whom he had issue a son, who died in infancy in March 1639; another, Thomas, sometime Deputy-Clerk of the Crown in Chancery; and three daughters: Sarah, Mary and Catherine.