Marcos C. Maldonado pleaded not guilty to five charges stemming from the alleged attack Dec. 2, according to the Los Angeles County District Attorney's Office.
The criminal complaint charges Maldonado with two felony counts each of rape of a child victim under 14 and sexual penetration by use of force on a victim under 14, along with one count of sodomy by use of force on a victim under 14.
The complaint alleges that Maldonado committed the offenses during the commission of a burglary and that he "engaged in the tying or binding of the victim or another person."
Maldonado was arrested Thursday in connection with the alleged sexual assault, Culver City police said last week.
Culver City police said officers responded around 7:45 a.m. Dec. 2 to the home on a report of a sexual assault that occurred between 2 and 3 a.m.
Maldonado had allegedly remained in the house until about 7 a.m., police said. Responding officers canvassed the area for evidence but could not locate the suspect. Investigators obtained surveillance video from the area showing the suspect leaving the area after the assault, authorities said.
"From the day that this crime occurred, detectives have worked tirelessly to identify and locate the involved suspect," police said in a statement. "... Through DNA evidence, the suspect in this case was identified and quickly arrested on the I-5 Freeway after leaving a downtown Los Angeles hotel and boarding a bus headed toward Bakersfield, California."
The mother of the 12-year-old girl who was assaulted told NBC4 that she awoke that morning to her daughter urging her to call the police.
"She's a soldier," the mother said of her daughter. "She's good on the outside. I think in time we will see what the damage is."
She told NBC4 it was unclear how the man had entered the home, but he had left through the front door.
Maldonado has remained behind bars since his arrest, jail records show.
He is due back Feb. 15 at the Airport Courthouse in Del Aire, when a date is scheduled to be set for a hearing to determine whether there is sufficient evidence to allow the case against him to proceed to trial.