The 26-year-old Boychuk had five goals, 10 assists and 43 penalty minutes in 51 regular-season games for Boston in his first full NHL season.
Boychuk, who earned $500,000 last season, could have become an unrestricted free agent. Financial terms of his new deal weren't released.
"I was thinking about maybe going to free agency and seeing what was out there. But when I looked around the league, I knew what kind of position I'd be in,'' Boychuk said. "To come back to Boston and the great coaching staff that we have there and all the guys there, it made it a lot easier decision knowing that we would have all these people back.
"That was the main factor that tipped the scales for me.''
Boychuk started last season as the Bruins' seventh defenseman. He was a healthy scratch for 23 of the club's first 26 games before he was assigned to Providence of the AHL for conditioning. He returned to Boston on Dec. 5 and missed only five games the rest of the season, an absence caused by a facial injury.
He had five goals and 15 points in the regular season. During the playoffs, he added two goals and six points in 13 games.
Boychuk, acquired from Colorado in June 2008, played in just one game for Boston during the 2008-09 season. With Providence, he had 20 goals and 65 points and won the Eddie Shore Award as the top defenseman in the AHL.
"He's made great strides this year. He was patient before he got in the lineup. He learned our system,'' general manager Peter Chiarelli said. "He's got a dimensional shot. He competes, he's got size. But the biggest thing that I saw was he's improved, going from being the defenseman of the year in the American League to our seventh D to start and working his way into our lineup, patiently but learning along the way.
"We have a very good defensive system and Johnny has picked it up and he's showed improvement while he's in the lineup.''