The third son of Sir Gerrard Napier, 1st Baronet, of More Crichel in Dorset, by Margaret, daughter and coheiress of John Colles of Barton, Somerset, he matriculated at Oriel College, Oxford, 16 March 1654, as a fellow-commoner. In 1673 he succeeded his father as second baronet, and settled down as a country gentleman.
He presented the college with a bronze eagle lectern. But, being in bad health, did not take a degree. Napier was knighted on 16 January 1662, and spent some time in traveling
He renovated Middlemarsh Hall and Crichel Hall, and represented Dorset in the House of Commons from April 1677 to February 1678, before he was unseated.
Napier sat as member for Corfe Castle in the two parliaments of 1679, and in those of 1681 and 1685-1687. In 1689 he took his seat in the Convention parliament as member for Poole, for which town he had procured the restoration in 1688 of the charter forfeited in 1687.
But a double return had been made for the second seat for that borough, and a committee of the House of Commons reported, 9 February 1689, that Thomas Chafin, who had a majority of the votes of the commonalty paying scot and lot, was entitled to the seat. The House, however, decided that the franchise should be confined to the "select body", id est (that is) the mayor, aldermen, and burgesses, who had voted for Napier by a majority of 33 to 22.
Napier continued to represent Poole till 1698.
He later sat for Dorchester from February 1702 until 1705. In 1697 Napier began to travel again, with a tour in France and Italy, keeping a journal. In October 1701 Napier revisited Holland, and in 1704 spent three months in Rotterdam, intending to go on to Hanover.
From March 1706 to September 1707 Napier was at Spa for his health.
And eventually died in England on 21 January 1709. He was buried with his ancestors at Great Minterne, Dorset, where he had erected a monument during his lifetime.
In 1656 Napier"s father married him to Blanch, daughter and coheiress of Sir Hugh Wyndham, justice of the common pleas. Lady Napier died in 1695, and, their first four sons having also died before 1690, Sir Nathaniel married a Gloucestershire lady, Susanna Guise, in 1697.
A daughter, Elizabeth, married Sir John Guise, 3rd Baronet of the same family.
Napier was succeeded by his only surviving son, Nathaniel, who was member for Dorchester in nine parliaments between 1695 and 1722.
His party affiliations in mid-life were unclear to contemporaries, but at the end he was an outright Tory.
