Juan Elias Garcia was arrested last week in Nicaragua, one day after the FBI added him to the famed list.
He is accused of killing his girlfriend, Vanessa Argueta, and their toddler son Diego four years ago.
Investigators say Garcia is a member of the MS-13 gang.
The 21-year-old Garcia was taken into custody Thursday near the U.S. Embassy in Managua, according to Nicaraguan police. He was immediately turned over to the FBI and extradicted on Friday. Nicaraguan authorities provided no further information about the arrest.
The FBI issued a statement Friday saying Garcia had surrendered and "voluntarily returned to the United States to face charges." His first court appearance was scheduled for Monday in U.S. District Court in Central Islip. It was not immediately known if he has an attorney.
Garcia was indicted on seven counts that included murder, murder conspiracy and firearms charges last month, shortly after he turned 21, and lost federal juvenile protection status that had prevented authorities from naming him publicly.
George Venizelos, the FBI assistant director of the New York field office, said earlier this week in announcing Garcia was added to the Most Wanted List that Argueta and Garcia had been in a romantic relationship.
Garcia, a native of El Salvador who authorities say was the first MS-13 gang member to make the bureau's most wanted list, allegedly brought Argueta to a wooded area of Central Islip in February 2010 after promising to take her to dinner, Venizelos said. The Treasury Department last year designated MS-13, or Mara Salvatrucha, an international criminal organization.
Argueta was accompanied by two other reputed MS-13 members who had received permission from the gang's leader to carry out the killing, Venizelos said. One of them shot her in the chest and head because of alleged threats made toward Garcia by rival gang members to whom she had ties, according to Venizelos.
Her son was also shot in the head twice - the second time after grasping at Garcia's leg - with the same .22 caliber handgun, he said.
Venizelos said in a statement Friday that placing Garcia on the Most Wanted List, and offering a $100,000 reward, helped crack the case.
"News media outlets, both domestic and abroad, displayed Garcia's photograph to members of the public hoping someone would turn him in," he said. "The pressure generated by this publicity was too much for Garcia to bear, resulting in his surrender and return to the United States."
MS-13 has a strong presence throughout the U.S., particularly in areas with substantial Salvadoran populations such as Southern California, the District of Columbia and northern Virginia. The gang also is allied with several Mexican drug cartels.
MS-13 is the largest and most violent street gang on Long Island, with more than a dozen chapters there, said Loretta Lynch, the U.S. Attorney for New York's Eastern District.
Rene Mendez Mejia, who pleaded guilty to the murders, and Adalberto Ariel Guzman, who was found guilty at trial, are awaiting sentencing, Venizelos said. Gang leader Heriberto Martinez, who allegedly sanctioned the killings, was charged in connection with the murders and other crimes and has been sentenced to three life terms, plus 60 years.
(The Associated Press contributed to this report)