The Scottish actor has played Dr Donald 'Ducky' Mallard on the CBS drama since 2003.
He has now agreed to a new two-year deal and will appear in the show's forthcoming tenth season, reports Deadline.
NCIS was officially picked up in March, along with 17 other CBS shows.
Several other cast members - including Michael Weatherly (Tony DiNozzo), Pauley Perrette (Abby) and Sean Murray (McGee) - are still negotiating new contracts, but are expected to return to the show.
The remainder of the series regulars - including star Mark Harmon (Gibbs) - already have deals in place to return.
The ninth season of NCIS continues on Tuesdays at 8/7c on CBS. In the UK, the series airs on Fridays at 9pm on FX.