Suspect Conrado Juarez was due in a Manhattan court Thursday. The cold case heated up just this summer.
The indictment hadn't been filed in court as of Wednesday. Defense lawyer Michael Croce said he hadn't yet seen it.
Juarez was initially arraigned on a murder charge after his Oct. 12 arrest.
The girl's body was found in a cooler by a highway in 1991. Detectives nicknamed her "Baby Hope." A tip recently led them to her name, Anjelica Castillo.
Juarez was her cousin.
Police say he confessed to sexually abusing and suffocating Anjelica. He told newspapers she died accidentally.