The fireballing closer was one of 111 players around Major League Baseball to file for salary arbitration on Thursday.
Technically, Youkilis was on that list as well, but his request for arbitration will be voided as soon as his contract is announced, which could be as early as Friday.
Left-handed reliever Javier Lopez was the third player from the Red Sox to file.
If the Red Sox can't reach contract agreements with Papelbon or Lopez by next week, salary arbitration figures will be exchanged between the players and the club.
Even if that ends up happening, expect the Red Sox to at least sign Papelbon and Lopez to one-year deals before arbitration is necessary.
This is Theo Epstein's seventh winter as the Red Sox's general manager, and he has never gone to arbitration.
Papelbon, who earned $775,000 in 2008, is likely to be in line for a sizable raise.
A three-time All-Star, Papelbon had another dominant season in 2008, posting a 2.34 ERA and a career-high 41 saves. Once again, Papelbon came up big in the postseason, firing 10 1/3 shutout innings.
As for Lopez, he was a consistent member of manager Terry Francona's bullpen in 2008, going 2-0 with a 2.43 ERA in 70 games.
Ian Browne is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.