The Manhattan district attorney's office told a judge Tuesday that Conrado Juarez has been indicted on an unspecified charge.
Juarez was initially arraigned on a murder charge following his Oct. 12 arrest.
The 4-year-old's body was found in a cooler alongside a Manhattan highway in 1991. Detectives nicknamed her "Baby Hope" and paid for her headstone.
A tip this summer led investigators to her name - Anjelica Castillo - and led to Juarez' arrest. He's her cousin.
Police say he confessed to sexually abusing and suffocating Anjelica. He later told newspapers she died accidentally and he only helped dispose of her body.
Juarez, 52, is being held at Riker's Island. He reportedly told prosecutors he no longer needs to be on suicide watch, but he now claims his confession was coerced by police.
Juarez spoke in a jailhouse interview, where he admitted helping a relative dump the body back in 1991. But he says he is not the killer.
In the confession, Juarez admitted to smothering the girl with her pillow to hide her screams while he sexually assaulted her.
It took 22 years to identify the body as Anjelica Castillo, who lived a short neglected life filled with abuse. Her relatives never reported her missing.
In the interview, Juarez expressed resignation over spending the rest of his life behind bars. His attorney says cops forced him to confess by depriving him of sleep.
Juarez, a restaurant dishwasher, is due in court to be formally notified that a Manhattan grand jury voted to indict him.