The 33-year-old right-hander went 12-12 with a 6.41 earned run average this year, including 0-2 with a 9.13 ERA in five September starts.
His season also was marred when he was named as one of three Boston starters alleged to have consumed beer in the clubhouse during games.
"He knows he's a much better pitcher than he showed in 2011," Cherington said. "We believe he's a much better pitcher and we're looking forward to have him on the staff in 2013."
Lackey is employed under a five-year contract he signed in December 2009.