The Penns have been a couple since 1989 and wed in 1996. They are the parents of two teenagers.
The movie stars have had a stormy relationship in recent years and filed for divorce twice before, then reconciled.
In her Aug. 12 petition, Wright Penn says they have already agreed to shared custody of their son, Hopper Jack, 16, and "have already agreed to division of all property," People.com reported Tuesday. Their 18-year-old daughter is starting college soon.
Wright Penn recently told More magazine she and her husband had no plans to continue working on their marriage.
"I hit that crossroad a while ago," she said. "I know what I don't want."
Sean Penn won Academy Awards for his work in "Mystic River" and "Milk."
His estranged wife is best known for her work in the "The Princess Bride" and "Forrest Gump."