The Oscar winner had been accused of mistreating son Maddox, 15, on board a private flight from France to Los Angeles.
Angelina Jolie filed for divorce soon afterwards and is seeking sole custody of their six children.
Social workers investigating the same claim cleared Pitt two weeks ago.
The FBI said: "In response to allegations made following a flight... carrying Mr Brad Pitt and his children, the FBI has conducted a review of the circumstances and will not pursue further investigation.
"No charges have been filed in this matter."
Pitt, 52, is seeking joint legal and physical custody of the couple's six children, three of whom were adopted by Jolie before the couple began dating in 2004.
Pitt and Jolie married just two years ago, in a private ceremony at their estate in Provence.