Armstrong, a contender for the U.S. Olympic Team, decided to return to the sport in 2011 after what she called an amazing experience in Beijing.
On Thursday, Armstrong was setting a "blistering pace" in the two-mile prologue course when she crashed. She was crying and holding her left shoulder after getting back on her bicycle according to the Associated Press.
Armstrong finished the course in 13th position, behind her closest rival for a spot on the U.S. Team cyclist Evelyn Stevens who finished 5th.
Armstrong's surgery on Friday morning will add pins and stabilize a mid-shaft clavicle fracture.
Even though it's a common cycling injury and one riders can recover from quickly, this puts a question mark on her hopes of riding in the London Olympics.
Before taking part in the prologue, Armstrong spoke about the USA Cycling’s upcoming announcement of the American Olympic team.
“We’re all waiting for that June 15 date to come so we can all take a deep breath,” she said. "I also think that having a strong spring behind me and having a consistency of performances I’m just going to go out and do my best and hope for the best.”
Armstrong just completed in the Amgen Tour of California last week.
The five-day Exergy Tour continues Friday with a 76.7-mile ride through wine country near the Snake River.