The black paint was found at the top of the number Wednesday, but it's not clear when the vandalism occurred. A team spokesman says the graffiti will be cleaned up.
Boston police are investigating. There have been no arrests.
Pesky was primarily a shortstop during his playing career. He had a six-decade association with the club as a player, manager, coach and broadcaster.
His number was retired in 2008. He died in 2012 at 92.