Steven Green, 21, a former private with the US Army's 101st Airborne Division, could face the death penalty if convicted.
It is the latest in a string of alleged atrocities to taint the image of US soldiers in Iraq.
The incident allegedly happened on March 12th with crime scene photos showing pictures of an Iraqi woman, an Iraqi male and a young girl, who all appeared to have died of gunshot wounds.
The court documents describe the incident in graphic detail and allege that the young girl was aged around five, while the rape victim was about 25.
But the Washington Post newspaper, which interviewed neighbours and investigated hospital records, put the girl’s age at around 15.
Private Green, formerly stationed in Fort Campbell, Kentucky, was arrested on Friday in the southern state of North Carolina.
Prosecutors alleged he was involved in the deaths near Mahmudiyah, south of Baghdad.
Private Green was honourably discharged from the army this year with a "personality disorder." He appeared in a US federal court in Charlotte, North Carolina, on Monday.
He is scheduled to appear in court again on July 10th in North Carolina, before eventually being transferred back to Kentucky, prosecutors in Louisville, Kentucky said.
Detailed allegations
The alleged incident only came to light on June 20th after a "combat stress debriefing" of other members of Private Green's unit.
Private Green belonged to the same unit, the 1st Battalion of the 502nd Infantry Regiment, as Kristian Menchaca and Thomas Tucker.
Both soldiers were kidnapped and their disfigured bodies later found on June 19th south of Baghdad.
The charges allege that "Green and three other individuals went to a house in the vicinity of Traffic Control Point 1, near Mahmudiyah, to rape one of the adult females living there.
"Green allegedly shot and killed an adult male, an adult female and a female child who were present in the house.
"The charges also allege that after participating in the rape of the second adult female, Green shot and killed her," the Justice Department statement said.
According to court documents, Green, and three fellow soldiers conspired to rape the woman, and changed into dark clothes before going to the house.
When they returned after the incident, they had blood on their clothes, which they immediately burned, the affidavit alleged.
Alleged rape and shooting
A soldier identified by the affidavit only as Source of Information Two
(SOI2) said he saw Green rape a woman then shoot her in the head "two-to-three times."
Another unidentified soldier cited in the affidavit alleged that Green and another identified person raped the woman, before Green shot her several times with an AK-47.
SOI2 alleged in the affidavit that Private Green had previously gone into a bedroom with other members of the family before gunshots were heard.
According to the affidavit, the source alleged that Provate Green came out saying: "I just killed them, all are dead."
As well as the four killings, Private Green was also charged with knowingly causing another person to engage in a sexual act by using force against them.
The Justice Department said Private Green was subject to civilian prosecution under the Military Extraterritorial Jurisdiction Act, which allows crimes committed in foreign countries by soldiers to be prosecuted as if they had been committed on US soil.
If convicted, Private Green could face execution for the murders or up to life in prison for the rape.