"The club and this merger have been 13 years in the making and we see this as another step forward for the game in Northland.
"The youth and senior sides have existed side by side over the last few years but this is the first time representative football in the region has been aligned so there is a clear pathway from 13th grade all the way through to first teams."
The FTC was established in Northland as part of the NZ Football Whole of Football Plan during the 2011 season.
The 2017 season was a breakthrough year for seven of the initial FTC graduates from six years ago, highlighting the success of the programme.
NFF CEO John Limna is excited by the alignment of the player development pathways in Northland.
"This is something we have wanted to do for a while and we believe this is the next step of the evolution of football in Northland," he said.
"We believe this will help take Northland FC and football in Northland to the next level."
Northland FC will take overall responsibility for the Youth teams from September 30.