Sir Christopher Hatton was the second son of William Hatton (died 29 August 1546) of Holdenby, Northamptonshire, and his second wife, Alice Saunders, the daughter of Lawrence Saunders (died 1544) of Harrington, Northamptonshire, and his wife, Alice Brokesby, the daughter of Robert Brokesby (died 28 March 1531) of Shoby, Leicestershire, and Alice Shirley.
Sir Christopher Hatton's early education is said to have been supervised by his maternal uncle, William Saunders (died c. 1583), but otherwise nothing is known of his life until he entered St. Mary's Hall, Oxford as a gentleman commoner at 15 or 16 years of age. Hatton left Oxford without taking a degree, and enrolled in the Inner Temple on 26 May 1560. No evidence exists as to whether he was called to the bar.
In 1561 he played the part of Master of the Game at a masque at the Inner Temple, and it was on a similar occasion that he first attracted the attention of Queen Elizabeth. Handsome and accomplished, and reputedly an excellent dancer, he came to court, according to Naunton, "by the galliard, for he came thither as a private gentleman of the Inns of Court in a masque, and for his activity and person, which was tall and proportionable, taken into the Queen's favour". In 1564 he became one of the Queen's gentlemen pensioners and a gentleman of the privy chamber, and in July 1572 was appointed captain of the yeomen of the guard. On 11 November 1577 he was appointed vice-chamberlain of the royal household and sworn of the Privy Council, and in the same month was knighted. In June 1578 the Queen formally granted him the Bishop of Ely's house in Ely Place, Holborn, despite the vigorous protests of the Bishop. These appointments, together with the valuable grants with which the Queen showered him during these early years, prompted rumours that he was her lover, a charge specifically made in 1584 by Mary, Queen of Scots. There was undoubtedly a close personal relationship between them. In correspondence, the Queen called him her "Lyddes", and he is said to have referred to himself in at least one letter as her "sheep". However, Hatton "was probably innocent in this matter."
Hatton represented Higham Ferrers in Parliament in 1571, and from May 1572 onwards was a member for Northamptonshire. He was an active agent in Parliament in the prosecutions of John Stubbs and William Parry. He was also one of those appointed to arrange a marriage between the Queen and Francois, Duke of Alençon, in 1581, although he urged the Queen not to marry Alençon.
According to one account Hatton had at one time assured Mary, Queen of Scots that he would fetch her to London if Queen Elizabeth died. Whatever the truth of this story, Hatton's loyalty to his sovereign appears to have been unquestioned, and on one memorable occasion in December 1584 he led 400 kneeling members of the House of Commons in a prayer for the Queen's safety.