Jagr, 39, the former NHL MVP who has spent the past three seasons playing in Russia, this week mulled over a one-year offer to rejoin the Pittsburgh Penguins, his original team, before ultimately deciding to play on the other end of Pennsylvania.
The Flyers' deal is worth $3.3 million. The Penguins' offer was for $2 million.
Before the Flyers deal was announced, Red Wings general manager Ken Holland told ESPN.com that Detroit also had pulled out of the bidding for Jagr.
Jagr was a Pittsburgh draft pick in 1990 and helped lead the Penguins to two Stanley Cup championships. The Penguins' hope was that he would accept the offer, play at least one season in Pittsburgh and then retire with the team he started with.
But Friday morning, before the Flyers announced the deal, the Penguins formally withdrew their offer.
"We made what we thought was a very fair contract offer to Jaromir on Tuesday, based on his stated interest of returning to the Penguins," Pittsburgh general manager Ray Shero said. "We made our best offer from the start, given our salary-cap structure, in an attempt to facilitate a deal. But now, after several days, with an extended time frame for making a decision and additional teams getting involved, we have decided to move in a different direction."
There were some departures from Philadelphia on Friday, as well. Free-agent forward Ville Leino signed to a multi-year contract with Buffalo, and forward Kris Versteeg was traded to Florida for two draft picks.
Leino finished fifth on the Flyers in scoring last season with a career-best 53 points (19 goals). From Finland, Leino now has 30 goals and 73 points in 149 career games split between the Flyers and Red Wings over four years.
Versteeg was acquired by Philadelphia from Toronto at midseason. He finished with 21 goals and 46 points on the season, but had only seven and four with the Flyers.
"Kris is a skilled young winger and a Stanley Cup winner that has scored more than 20 goals in each of the last three seasons and will make an immediate impact on our team," Panthers general manager Dale Tallon said. "He is versatile enough to play any forward position and brings passion and commitment to the rink every single day."
For Versteeg, the Flyers acquired a conditional second-round draft pick in 2012 or 2013, and San Jose's third-round pick in the 2012, which was previously acquired by the Panthers.
Jagr will be looked upon to replace some of that scoring punch. He has 646 career NHL goals, and when he slips on that orange-and-black uniform for the first time this fall, he will be the NHL's active scoring leader with 1,599 points.
"Jaromir is one of the greatest players in Penguins history," Shero said, "and we wish him all the best."
A Czech native, Jagr won an Olympic gold medal in 1998 and a bronze in 2006. He also won two hockey world championships, in 2005 and 2010.
Jagr's agent is former NHL defenseman Petr Svoboda, who, interestingly enough, played five seasons with the Flyers.
Information from ESPN.com's Scott Burnside and The Associated Press was used in this report.