The Marine has been identified as Private First Class Avery Rosario, according to NBC News.
PFC Rosario's defence attorneys said he met the girl on Tinder and claimed she had listed her age as 21 on the dating app.
Two of the charges against PFC Rosario were referred to a general court-martial by Brigadier General Andrew Niebel, who commands the 1st Marine Logistic Group, according to a spokesman for the unit.
PFC Rosario appeared before the court-martial on Thursday, according to Captain Virginia Burger.
The situation began on 13 June when the girl's grandmother reported that she had gone missing. The girl had reportedly left home on 9 June, and had run away before, but had never been gone more than a few days, according to the grandmother.
The girl was located on 28 June, more than two weeks after her grandmother reported her missing. She was found at Camp Pendleton in PFC Rosario's barracks, according to a police report.
Shortly after the girl was found, her aunt told police that her niece had been sold to the Marine for sex, according to NBC 7 San Diego.
In a TikTok video, the aunt claimed that her niece had "learning disabilities" and said the entire facility was complicit in the girl's assault.
“The security looked her in the face and allowed this man to bring a minor on to base where he then proceeded to have sex with her" the teen's aunt said. "Due to her age, she could not have given this consent.”