Family traditon attributes the name to a commendation given a young knight of Willam the Lion. After showing particular valour and bravery William the Lion is said to praised him sayiong his valour had "nae peer".

The Napiers held lands at Kilmahew for 18 generations until the lands were sold in 1820. Alexander Napier was the prosperous merchant of his time and was Provost of Edinburgh. With his great wealth he acquired the lands of Merchiston in 1436. In 1440, King James II made Alexander's son Comptroller of the Royal Household in thanks for his part in rescuing his mother from rebels.

This Napier's son and grandson were both killed at the Battle of Flodden in 1513 and another Napier heir was killed at the Battle of Pinkie Cleugh in 1547.

Perhaps the best known Napier was the 7th Laird of Merchiston, John Napier who developed the system of logarithms. His son, Archibald, accompanied James IV to London when he claimed the throne of England. He was to become a member of the Privy Council as well as Lord Justice Clerk of Scotland, Baronet of Nova Scotia in 1627 and finally made Baron Napier of Merchiston later in 1627.