Wilson did not play in the team's 44-21 loss to Oregon on Saturday. He had suffered a concussion in a 20-19 loss to Arizona State a week earlier.
An initial scan for the concussion turned up evidence of a preexisting head trauma and a follow-up angiogram confirmed it. Whittingham did not give further details about the condition, but said it was not life-threatening.
It is not known if the condition will cut short Wilson's career. The team will not have a definitive answer for several months on whether Wilson can return.
"Travis is a tough and competitive kid," Whittingham said. "He's really upset by this, obviously, and disappointed to say the least. He's a big part of what we're doing on offense. He's our starting quarterback and we're going to miss him. But the most important thing is his long-term health."
This is the fourth straight season Utah has lost a starting quarterback to a season-ending injury. The Utes have not had the same quarterback start and finish a season since current assistant coach Brian Johnson led the team to the Sugar Bowl in the 2008 season.
Adam Schulz will take over as Utah's starting quarterback for the remainder of the season. Schulz, a former walk-on, made his first start against Oregon last weekend. The sophomore threw for 181 yards, a touchdown and an interception on 13-of-30 passing against the Ducks.
Freshman Connor Manning, who is redshirting, will move to No. 2 on the depth chart. Whittingham said Manning will not see playing time, however, unless an emergency arises.
Wilson's season-ending injury caps a frustrating season for the sophomore quarterback. He missed parts of games against USC and Arizona with an injury to his throwing hand. Wilson struggled with consistency while battling his injuries, throwing for 187 yards, six interceptions, four touchdowns and completing just 14-of-44 passes in his final three starts.
He will remain with the program while awaiting a more definitive diagnosis on the nature of his head trauma. And Wilson's teammates want him to know they will be there to support him.
"The team is just going to really come around him and help him out in this situation," Utah tight end Jake Murphy said. "Despite what people think, football isn't life."
Utah (4-6, 1-6 Pac-12) will play at Washington State (5-5, 3-4) this weekend.
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