Freer, 22, was the Knights’ Players’ Player of the Year in 2011 but has now returned to Huntington Stadium on a deal which will keep him at the club until the end of 2013.
Player-coach Chris Thorman said: “We never wanted to lose Nathan but we respected his decision to join Featherstone last year.
“We are delighted to welcome him back as he is a fantastic player as well as been a top professional. We know he will fit in well with the ethos we have at the club and I am looking forward to working with him again.”
Freer came through the academy ranks at Hull, spending time on loan at Doncaster before switching to York in 2009.