San Diego manager Bud Black said that Hill had the surgery on Wednesday in Birmingham, Ala., where orthopedic surgeon James Andrews performed the procedure. The anticipated recovery time is between 10-14 months.
"He had the ulnar collateral ligament in his elbow reconstructed. He is in the early stages of that, in the brace," Black said. "In time, [he'll] start the long process of rehabbing that surgery. He's been through that before."
During the surgery, a new ligament was created from a tendon in Hill's hamstring.
Hill has been on the disabled list since April 26 with inflammation in his right elbow. It was determined in early May that there was no ligament damage in the elbow. He threw two bullpen sessions earlier this month. That's when the elbow tightened up on him.
Hill was transferred to the 60-day disabled list on June 14, though the Padres were hoping surgery wouldn't be needed.
Hill wasn't available for comment.
"Like most professional athletes, he's going to endure," Black said. "He feels that the pain he has had the past couple of years. They found some calcification, some bone in the ligament that they removed.
"The process starts again. So now I think they realize where the pain was originating. Hopefully, that has been relieved."
Hill started three games for the Padres before going on the disabled list. He was 1-1 and had a 5.25 ERA. The Padres signed Hill to a Minor League contract on March 23, and he made the Opening Day roster as the fifth starter.
Hill has been beset by injuries since 2004, when Andrews performed first performed ligament replacement surgery on him. Three years later, Hill had surgery to decompress the radial nerve in his right forearm as well as to clear out scar tissue in the elbow.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.