Craig Brewster had initially hoped to snap up the Irish Under-21 international on a loan deal, but after the player impressed on the club's pre-season tour of Denmark, decided to offer him an extended contract.
Rooney, who scored a hat-trick on his league debut for Stoke City in 2006, is looking forward to getting started in Inverness.
He said; "I am really pleased to be here after enjoying my time with the squad in Denmark. I am desperate to prove myself at SPL level and can't wait to get playing."
Joining Rooney at Caley Thistle will be Ugandan midfielder Dan Wagaluka, who will spend a week on trial in Inverness.
Brewster meanwhile has decided to drop his interest in former Ajax and Hercules winger Kiran Bechan, admitting "it is very unlikely he will be coming back."