Hernandez was arrested in 2012 following a tip to detectives. He had told family members he killed a child in New York, CNN reported at the time.
The first trial ended in 2015 with the jury failing to reach a unanimous verdict.
At trial, Hernandez was accused of luring Patz into the basement of the store with the promise of a soft drink, choking him and putting his body out with the rubbish.
While there was no material evidence against him, Hernandez confessed to the killing in 2012. He later retracted his confession and pleaded not guilty.
A defence lawyer previously said Hernandez is innocent and has an IQ of 70, which puts him in the bottom 2% of the population.
“The District Attorney has determined that the available, admissible evidence supports prosecuting defendant on the charges of murder in the second degree and kidnapping in the first degree in this matter, and the people are prepared to proceed,” said the letter seen by AFP.
In the letter to Judge Ellen Biben, Manhattan prosecutors said they were ready to discuss a retrial during a hearing scheduled for December 1.
Etan’s disappearance shocked Americans and fuelled a generation of hyper-vigilant parenting.
His parents only discovered he was missing after he failed to come home from school at the end of the day. His body was never found, and the case was one of the city’s great unsolved crimes for decades.
Photographer Stan Patz’s pictures of his son were the first of a missing child to be featured on milk cartons as part of a nationwide search.
-Agence France-Presse