Authorities said Audrii had been missing since Thursday, Feb. 15, when she did not make it to her school bus that morning.
Investigators found the 11-year-old's body six days after the Amber Alert notified Texans of her disappearance.
Polk County Sheriff Byron Lyons did not disclose the condition of Audrii's body, which the Harris County Institute of Forensic Sciences received for an autopsy.
On Thursday, the medical examiner's office said Audrii died from homicidal violence including blunt head trauma. Officials did not provide further information.
SEE MORE: 11-year-old Audrii Cunningham's body found in Trinity River, Polk Co. Sheriff says
Don Steven McDougal was first named as a primary person of interest in the case and later a suspect in her murder.
Polk County District Attorney Shelley Sitton said McDougal is charged with capital murder of a person equal to more than 10 years old but less than 15 years old.
McDougal was already in custody on an unrelated aggravated assault with a deadly weapon charge.
McDougal was said to be a friend of Audrii's father, allowed to live in a trailer behind their Livingston house.
According to Lyons, McDougal admitted to leaving the house with Audrii the morning she disappeared but would not tell investigators what happened next.
SEE MORE: Family friend charged with capital murder in Audrii Cunningham's death
SEE MORE: Previous child victim of man charged in Audrii Cunningham's murder says system failed her and Audrii
Previous child victim of man charged with Audrii Cunningham's murder speaks