The Stark’s Park gaffer has six graduates from the academy as part of his first team squad; Aaron Arnott, Greig Young, Kyle Bow, Quinn Coulson and Kieran Mitchell, along with first team regular, midfielder Dylan Tait.
But, with the structure set to collapse at the end of the year, the path for up and coming youngsters in Fife from Elite to full-time football may not be as smooth in the future.
McGlynn says he is confident the club will come up with a solution to the problem but also expects it will take “years” before Raith Rovers will see the full benefit, with youngsters making that progession to first team level.
“Dunfermline have decided to go their own way,” he said. “They've had an injection of money from Germany from investors, so they're planning to go in one direction and it left a void that couldn't be made up financially.
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“At Raith Rovers, we will have to take our time, but not too long. I think we will have to assess what we are going to do.
“We went down this route in the first place after I had left the first time I was here (in 2012) with the four Fife teams amalgamating and it's now going to leave a massive void for Raith Rovers to try and pick up.
“It's not going to be a quick fix for us. It's not going to be a five minute job – it's going to take years. It's going to be a slow burner to pick this up and try to get it back to how it is as the moment.”