First Lieutenant Ehren Watada was charged on Wednesday with missing movement, contempt towards officials and conduct unbecoming an officer, the army said in a statement.
Watada called the war and US occupation of Iraq "illegal" and said participation would make him party to war crimes.
But the army said: "Officers are held to a high moral and legal standard. Acts contrary to this standard may be tried by court martial."
Watada's supporters say he is the first commissioned US officer to publicly refuse to serve in Iraq and face a military court.
He remained at Fort Lewis base in Washington state when his unit shipped out to Iraq on June 22.
Watada said he would be willing to serve in Afghanistan or elsewhere.
If found guilty of all charges, he could face several years in prison, dishonourable discharge and forfeiture of pay, according to the army.
Watada's lawyer, Eric Seitz, said he expected the missing movement charge, but was somewhat surprised by the other charges, because they raise free speech issues.
"What he said about the war and the way the war began and the misrepresentations by the Bush administration are all true.
"Not only does he have a right to make those statements, he has an obligation to make those statements."