Earlier, Melton wrote on Twitter: "Good to be a Bear for another year," before adding, "Hopefully we can get a long-term deal done soon!"
The franchise tag for defensive tackles in 2013 comes with a guaranteed salary of $8.45 million.
By tagging Melton, the Bears give themselves time to work out a long-term deal with him, similar to the way the club tagged Matt Forte prior to signing the running back to a four-year deal in July 2012.
"Henry has been a good player for us and we are using the franchise tag so his development continues as a Bear," general manager Phil Emery said. "We will continue our conversations with Henry and work toward a multiyear agreement."
With the salary cap for the 2013 season now officially set at $123 million, the Bears will operate with approximately $12 million in cap space at the start of the new league year. Minus restructuring contracts for some of their big-money players, the Bears now have used a large portion of their cap space by tagging Melton. That's not even taking into account the cap room the Bears would need to sign their rookie class or what it would take to bring back some of their own free agents such as linebacker Brian Urlacher or guard Lance Louis.
Melton tied for third among NFL defensive tackles last season with six sacks, and he also forced two fumbles. He plays one of the key positions in the Bears' scheme.
In the past two seasons, Melton has 13 sacks, second among defensive tackles in the NFL during that span.