Kukkonen had five goals and nine assists in 74 games for the Flyers and the Chicago Blackhawks last season. The defenceman led all NHL rookies in blocked shots with 151.
"He showed that he can move the puck extremely well and that he is a really steady defender," said Flyers general manager Paul Holmgren. "We look forward to him being part of our defence for the next two seasons."
The NHL-worst Flyers also signed wingers Scottie Upshall and Ben Eager to two-year deals in the last week as they try and build their way back through younger players.
The Flyers also signed right-winger David Laliberteto to a three-year entry-level contract. He was originally drafted by the Flyers in the fourth round (124th overall) of the 2004 entry draft.