Pedro Hernandez was arrested a week after what police and prosecutors believe was the last of at least three assaults of the girl on separate occasions at Sanchez Elementary School in the Mission District.
On June 3, a teacher's aide at the school became suspicious of Hernandez's behavior toward the girl after he arrived to bring her lunch around noon, according to police. She later caught Hernandez allegedly assaulting the girl inside a secluded stairwell at the school and called police.
Hernandez left before police arrived but was arrested June 10 at a homeless shelter at St. Bruno's Catholic Church in San Bruno.
The sexual assault was recorded on the school's video surveillance system, police said.
Hernandez, who is being held on $2 million bail, pleaded not guilty this morning in San Francisco Superior Court to seven felony counts, including continuous sexual abuse of a child, sexual intercourse or sodomy with a child, and oral copulation or sexual penetration with a child. The last two charges are punishable by life in prison.
A judge also granted a restraining order forbidding Hernandez from visiting or contacting the alleged victim, the family's Bernal Heights home and the school. Hernandez's case returns to court for a scheduling hearing on July 8.
Prosecutor Marianne Barrett said today that Hernandez, who collects recycling for a living, had been staying with the girl's family at the time of the alleged assaults. He is believed to be originally from Mexico and federal authorities have requested an immigration hold.
According to Barrett, Hernandez is believed to have assaulted the girl at least two other times at the school. Police are now reviewing earlier surveillance footage.
Following the latest alleged incident, prosecutors obtained a $2 million warrant for his arrest and police alerted state, U.S. and Mexican authorities.
According to Barrett, Hernandez had told his family he was headed back to Mexico. Police were able to nab him in San Bruno by tracking his phone records, she said.
"I'm just very happy that we were able to apprehend him before he fled to Mexico," Barrett said.
Two of Hernandez's adult children are accused of harboring him after the warrant was issued, and are facing charges of being an accessory to the crime after the fact. They are being held on $100,000 bail each.
Hernandez's newly appointed attorney Jose Umali said after court today that it was difficult for him to comment on the case, having just met his client and begun to review the evidence. He agreed the charges are "very serious" but said Hernandez "seems like a very gentle person."