Conrado Juarez, 52, was arrested on a murder charge and was awaiting arraignment, Police Commissioner Raymond Kelly said. He was 30 at the time of the girl's death.
It wasn't clear whether Juarez had a lawyer. Police said he lived in the Bronx, but that the family had been living in Queens at the time of the killing. They also said Juarez claimed that a relative helped him dispose of the girl's body.
Anjelica Castillo's naked, malnourished corpse was discovered on July 23, 1991, beside the Henry Hudson Parkway. Detectives thought she might have been suffocated but had few other clues as to what happened.
The case became an obsession for some investigators. Hundreds of people attended a funeral for the unknown girl in 1993. Her body was exhumed for DNA testing in 2007, and then again in 2011.
In July, detectives tried another round of publicity on the 22nd anniversary of the discovery. They canvassed the neighborhood where her body was found, hung fliers, circulated sketches of the girl and a photograph of the cooler and announced a $12,000 reward for information leading to an arrest.
Former detective Jerry Giorgio, who had the case from 1991 until his retirement over the summer, said he remained confident the case could be solved. Assistant Chief Joseph Reznick, who also worked the case, said they never gave up.
"I think reflecting back on what we named this little girl, Baby Hope, I think it's the most accurate name we could have come up with," Reznick said.
Giorgio left the NYPD and went to the Manhattan district attorney's cold case squad, from which he retired this year. "I missed the tipster call by a couple of weeks, damn it," he said.
The tipster led police to Anjelica's sister, who told detectives her sister had been killed. Police matched DNA from Anjelica to their mother. The mother, who was not identified, didn't have custody of Anjelica at the time of the girl's death - she had been living with an aunt on the father's side, Bavlina Juarez-Ramirez, police said.
Police closed in on Juarez and waited for him Friday outside a Manhattan restaurant where he worked as a dishwasher. He told them he killed the girl at the apartment of his sister, Juarez-Ramirez.
"When she went motionless, he summoned his sister from another room," Kelly said.
Then, the sister, who is now dead, got the blue cooler and helped dispose of the body. Kelly said they took a livery cab from Queens to Manhattan where they dumped the cooler, then separated.
The cooler, which contained the girl's remains and unopened cans of Coke, was later discovered by construction workers.
Kelly called the arrest a superb case of detective work, and he was proud of his officers. Juarez was being held on murder charges and was awaiting arraignment.
"For me, it makes you proud to be a member of this organization - they were unrelenting."
The detectives assigned to the case were instrumental in organizing a burial in a Bronx cemetery for the girl in 1993. Hundreds attended the funeral; Reznick gave the eulogy. The girl was dressed in a white frock and buried in a white coffin.
The detectives paid for the girl's headstone that reads: "Because we care."
On the tomb sit two little angels.