The defender has been a regular in the side since moving to the Scottish Premier League outfit in the summer.
Manager Terry Butcher told the club's website: "Gary Warren has signed a new two-year deal. We are delighted because he is an important member of a very strong defence and he is playing the best football of his career.
"Apart from the Dundee United game when he was suspended, he has played in every minute of the previous 34 matches. He has got six goals as well which is impressive for a defender. He's a first-class defender and is improving all the time.
"I think it sends out a signal to a lot of people, if you come up here, see the place, play football for us, you'll soon come to love the place. You will enjoy your football and your life as well."
The 28-year-old joined Inverness from Conference side Newport County.