Financial terms of the contract were not released but multiple media reports placed the total value at $30 million.
"We kind of hashed it out a couple different ways," MacDonald told NHL.com. "Ended up finishing on six (years), and I felt like a good, long-term commitment was great for me and they agreed with it. Obviously it's a big commitment for them, a big commitment for me. It's a good deal."
The 6-foot-1, 190-pound MacDonald was acquired by the Flyers from the New York Islanders on March 4 in exchange for forward Matt Mangene, a third-round pick in the 2014 NHL Entry Draft, and a second-round pick in the 2015 NHL Entry Draft.
MacDonald, 27, appeared in 19 games for the Flyers, recording four assists, while averaging 22:00 in ice time per game. MacDonald led the NHL this season with 242 blocked shots, which was 41 more than his closest competition. In 82 total games with the Flyers and Islanders this season, MacDonald recorded four goals and 24 assists for 28 points.
A native of Judique, Nova Scotia, MacDonald was drafted by the Islanders in the sixth round (160th overall) of the 2006 NHL Entry Draft.
The Flyers will take on the New York Rangers in the first round of the 2014 NHL Stanley Cup playoffs starting Thursday.
"You try not to think about it (the contract) too much," MacDonald said. "With the playoffs coming up and everything, it's nice to get it out of the way and concentrate on making a run."