The management duo who rejoined the club for a second spell in 2018 will depart Stark's Park when their current deals expire this month, saying their decision was made with “a heavy heart”.
It is widely expected that the pair will join League One side Falkirk.
McGlynn and Smith led the club to the League One title in the truncated 2019/20 season before finishing third in the Championship last year and reaching the Premiership play-off semi-final where they lost to Dundee.
This time out they finished the season in fifth place in the league table, missing out on a play-off position.
They were winners of the SPFL Trust Trophy but McGlynn become embroiled in the controversy over the signing of David Goodwillie in January which came as the club were in the middle of an 11-game winless run which would ultimately cost them a place in the top four and the chance of promotion to the Premiership.
It was their second spell as the management team in Kirkcaldy, having previously been at the club from 2006-12 before McGlynn left to take over at Hearts, whilst Smith remained at Stark’s Park as number two to Grant Murray.
A statement from the pair read: “It is with a heavy heart that we announce we will not be extending our contracts with the club.
“It’s been a privilege and a pleasure to work at this great club, Paul and I have had a great time in the last three years and nine years in total with many successes – two league title, two challenge cup wins – in Paul’s case a third cup win – as well as developing youth players to achieve their ambitions.
We would like to go on record to thank the fans for their magnificent support both home and away, we have always had a great rapport with them.
“We would like to thank our backroom staff, CEO, office staff, ground staff, cleaning staff and all volunteers for their hard work, professionalism, attitude and genuine enthusiasm.
“The players for their ability, tactical awareness, hours upon hours on the training pitch, hours of video analysis and for their commitment and dedication,they have been a joy to work with.
“We would like to thank the directors for giving us the chance to come back to the club three years ago, and for their continued support.
“We leave the club in a far better place than when we arrived, there is a good squad of players and with additions this summer, they can be a great team and we wish everyone Raith Rovers minded all the very best going forward.”
Speaking to the FFP before his departure, McGlynn added: “There’s a good squad of players here.
“It needs additions like every team does, there’s no team that goes into the following season with the same set of players.
“We got silverware and finished fifth. It you average that out that’s two fourth place finishes over two seasons.
“You would maybe have taken that, but it was a difficult season with a number of players suffering long-term injuries.
“We’re not delighted with it because we pride ourselves on improving, but we did get some silverware and there are five teams in that league who would love to be where Raith Rovers are.
“We showed on Friday against the league champions how good a team we are, so there’s no reason why, with some good additions, that Raith can’t be pushing again next season.”
It is understood that McGlynn may try to take some of Raith’s out of contract players with him to the Falkirk Stadium, with captain Kyle Benedictus and Brad Spencer among them.
A statement from the Raith board wished the departing duo all the best.
“We offer our thanks to John and Paul for their service to the club, and salute their achievements since returning to Stark’s Park in September 2018.
“The board can also confirm that we will be actively looking to appoint a new management team to take the club forward, and will be starting the recruitment process with immediate effect.”
Names thought to be in the running to take over include former Dundee boss James McPake and Craig Levein who had a short spell as Raith boss in 2006 and upon his departure for Dundee United recommended McGlynn to be his successor.