"I'm not counting on coming back," Francis said Thursday.
Francis said Rockies orthopedic surgeon Thomas Noonan will perform the operation Wednesday, and Francis expects rehabilitation to take six to 12 months.
Francis, a vital part of the Rockies' run to the World Series in 2007, spent a stint on the disabled list last season before being shut down early in September. He pitched with pain in his throwing shoulder that started in May and went 4-10 with a 5.01 ERA.
MRIs haven't shown a clear-cut problem.
He came to spring training hoping to test his shoulder before making a decision on what to do next and reported feeling less discomfort in camp. But Francis changed his mind after watching video of his pitching form in a Tuesday bullpen session.
"It didn't look anywhere close. I was really disappointed," Francis said. "There is obviously something going on."
He said he spotted changes he had made in his delivery to avoid pain.
"I had no arm speed, my arm was short and the arm action was short and I was not powerful at all," he said.
Francis said it was bad time of year to make the decision, but "I think it is a necessary one."
"I could put damage on something else. I could put strain on an elbow," he said. "I just want to go out there and be the pitcher I can, and I don't think in the state I am in right now I could do that. It would not be fair to me and it would not be fair to the team."
Francis was 17-9 with a 4.22 ERA in 2007 and is 51-44 with a 4.74 ERA in five seasons with the Rockies.
But Colorado entered camp not counting on having him in the rotation for the start of the season. Aaron Cook, Ubaldo Jimenez, Jorge De La Rosa and Jason Marquis are considered the nucleus of the starters, with a fifth spot still to be determined.