Around 1642 he married Lady Elizabeth Erskine (d. 1683), the eldest daughter of John Erskine, 19th (or 3rd) Earl of Mar. They had five children:
Archibald (d. 1683), who succeeded as 3rd Lord Napier.
John (d. 1672)
Jean, who married Sir Thomas Nicolson of Carnock, whose son, Thomas (1669 – 1686), became the fourth Lord Napier.
Margaret (d. 1706), who became Lady Napier, fifth holder of the title in her own right (whose grandson, Francis (1702–1773), became the sixth holder of the title as the sixth Lord Napier).
When in 1650 he sought to return to his home in Scotland, he asked permission of King Charles to rejoin his uncle, and this was granted. However, before he could return, Montrose was captured, tried and executed. Lord Napier decided against returning to Scotland.
Due to his unflagging Royalist support, he was notably excepted in the act of grace and pardon by Oliver Cromwell on April 12th 1654. He died at Delfsham in Holland in the beginning of 1660, so did not live to see the Restoration.