Sir Henry Vaughan the younger (1613 – 26 December 1676), of Derwydd, Llandybie in Carmarthenshire, was a Welsh Member of Parliament.
He was the son of Sir Henry Vaughan the elder, a long-serving member of Parliament and leader of Royalist forces in Carmarthenshire during the English Civil War.
Sir Henry had acquired the Derwydd estate by marriage to his wife Sage.
In April 1645, he was defeated by Cromwell in a minor engagement at Bampton in the Bush, and he was captured at Tenby in 1648.
On his death he was buried in Llandybie church and was later succeeded at Derwydd by his nephew, Richard Vaughan.