The 38-year-old "Monster" Oscar winner was hurt while making the action flick "Aeon Flux" in 2004.
"Charlize got injured on a set and broke a vertebrae years ago," an insider told UsMagazine.com. "It's been bothering her a lot lately so she had surgery to correct it and they had to go through her neck. ... She will be totally fine."
Theron has not publicly spoken about her operation and wore a scarf around her neck to Variety's 5th annual Power of Women event in Beverly Hills Friday.
"She's got a small Band-Aid on her neck," a second source said. "She kept fussing with the white scarf she [was] wearing to cover it."