Whitehead is a midfielder who re-joined Leek Town in January 2018 after a spell with NPL Premier Division outfit Matlock Town.
He originally signed for Leek at the start of 2015/16 season from Rainworth Miners Welfare, making 13 appearances.
Since then he has played for both Lincoln United and Spalding United, helping both sides to the promotion play-offs.
Whites` manager Sam Wilkinson told the club`s website: "He’s another very good addition to the squad and another with great physical presence.
"He's leader who has got great experience in the league, having made it into the play-offs with us and Spalding.
"He has played at a higher level representing Matlock.
"He has also played at Leek where he narrowly missed out for on three consecutive play-offs.
"Nathan feels he’s got a lot of people to prove wrong from last season and has that hunger to achieve, which we need at Lincoln United.
"He wants to achieve something at the club and becomes my fourth very good addition this season.”
However, having previously agreed to remain with the club, Luke Hornsey and Charlie Ward have had to move on as they cannot fully commit due to work commitments and family reasons respectively.