The 26-year-old, who is the brother of Manchester United striker Wayne, arrived at the West Yorkshire club in February, scoring one goal in seven appearances.
Rooney has also had previous spells playing in the United States with New York Red Bulls and Orlando City.
"He has a desire to help improve us as a club," said manager Adam Lockwood.
Rooney's only Guiseley goal came on his debut against Sutton United on 14 February, which gave him a total of 12 in the National League before his season was ended by injury.
Attacking midfielder John Rooney will join Guiseley on a permanent basis after his loan spell from Wrexham.