Pedro Hernandez, 51, of Maple Shade, N.J., was indicted by a New York City grand jury in the death of Etan Patz, attorney Harvey Fishbein said. Hernandez was arrested earlier this year, and investigators say he confessed.
The district attorney's office would not comment.
Etan's disappearance led to an intensive search and spawned a movement to publicize cases of missing children. His photo was among the first put on milk cartons, and his case turned May 25 into National Missing Children's Day.
The case has stymied investigators - and Etan's devoted family - for years.
Another man was long ago found civilly responsible for Etan's disappearance but never criminally charged because of a shortage of evidence.
Jose Ramos, now 69, had been dating the boy's baby sitter in 1979 and was considered a suspect. He was later convicted of molesting two different children and is in a Pennsylvania prison.
But investigators began focusing on Hernandez this year after a tipster called police about comments by Hernandez's sister that she heard secondhand he told a church prayer group in the 1980s that he killed a child in New York City.
Hernandez, now a married father, was a teenage stock clerk at a convenience store when Etan disappeared on his way to school on May 25, 1979. Police say Hernandez told investigators he lured the boy into the convenience store with the promise of a soda.
He allegedly said he led the child to the basement, choked him and left his body in a bag of trash about a block away. The convenience is now an eyeglass shop, and city records pinpointing where garbage was dumped don't go back that far.
Fishbein has described Hernandez as bipolar and schizophrenic, with a history of hallucinations. The diagnosis could become the basis of psychiatric defense claiming that Hernandez agreed to speak to police without understanding his rights, and that the purported confession was a sick fantasy.