Even Star Editor Dennis Ryerson said he was caught off guard by the resignation.
Her departure is effective Aug. 1. Henry, 55, did not indicate why she was resigning, but said in her note to staffers that she would be taking time off.
"My sense is, she just felt it was time," Ryerson said.
Henry's resignation and the resignation of Louisville Courier-Journal Publisher Denise Ivey coincide with an announcement by Gannett today that it is restructuring its U.S. Community Publishing Division. As part of the reorganization, five regional groups will become four.
The changes at Gannett come at a tumultuous time for the newspaper industry. Daily newspapers are experiencing declining circulation and sagging ad sales. Though they also have expanded their Internet news sites, those efforts so far have provided only a modest revenue boost.
Henry said in her note to staffers that her replacement would be named in two to three weeks.
Ryerson said it's business as usual in the newsroom.
"I don't anticipate any change in what we're doing because in part we've had good success with our initiatives," Ryerson said.
Henry took over as Star publisher from Dale Duncan in 2000. Henry has been at Gannett since 1974, starting in the newsroom of the Reno (Nev.) Gazette Journal. She helped launch USA Today in 1982, then returned to Reno as executive editor. In 1996, she became publisher of the Des Moines Register, a position she held until accepting the top post in Indianapolis.
In April 2005, Henry was tabbed to head the Interstate Newspaper Group, which includes Gannett publications in Indiana, Kentucky, Ohio and Tennessee.
Earlier this year, Henry was mentioned as a possible replacement for Sue Clark-Johnson, the outgoing head of all Gannett newspapers. Ultimately, Henry was passed over for that job.
In her e-mail to staffers, Henry touted numerous gains during her tenure, including growth of online properties and the launch of niche publications.
Her successor likely will face a major challenge later this year. The union contract that governs many of the Star's newsroom employees expires in December. Many employees expect a protracted contract fight.