The 60-year-old turned down the offer of a new contract from the Stark’s Park side and has dropped to League One to spearhead the Bairns promotion push next season.
The Scotsman has learned that McGlynn is also attempting to take a number of out-of-contract Raith players with him, with captain Kyle Benedictus and influential midfielder Brad Spencer among those on expiring deals at the Kirkcaldy club.
"I'm delighted to be here," McGlynn said. "It's been out in the public domain for a little while so it's not exactly breaking news, but we're delighted to be at Falkirk.
"We appreciate the task in hand as it's a big job and a big football club, but we're excited at the prospect of trying to get it back where we think it should belong."
Smith added: "I had a short spell as a player here 30 years ago so I know how big a football club this is. It's up to John and myself to push on and try to get the team back up there."
McGlynn guided Raith to a fifth-placed finish in the Championship this season, missing out on a place in the promotion play-offs for a second consecutive season by just two points, as well as lifting the Challenge Cup trophy.
However, he also endured a difficult spell following the decision to sign David Goodwillie in January, a move which led to an angry outcry among supporters, boardroom resignations and an embarrassing U-turn from the club.
The former Hearts and Livingston boss was in his second spell in charge at Stark's Park having guided Raith to the old Second Division title in 2008-09, a feat he repeated in the coronavirus-shortened 2019-20 campaign, finishing a point ahead of Falkirk when the season was stopped.
Raith, who have been praised for the brand of football played under McGlynn, had hoped to convince their boss to stay, but he has been tempted by challenge of reviving a Bairns side that has hugely underperformed in recent years.
Falkirk finished fifth in League One this season, and parted company with boss Martin Rennie last month, having sacked Paul Sheerin earlier in the season.
They will hope McGlynn can be the man to get them back up into the second tier at the third time of asking.