Police charged Rian Rodriguez as a fugitive of justice. He was found with 17-year-old Caitlyn Frisina Friday near Syracuse.
Authorities believe Frisina left with Rodriguez voluntarily a week ago.
Rodriguez, the girl's soccer coach, has been remanded in Onondaga County and could face federal charges.
Frisina is now back with her parents in the Syracuse area.
Authorities in Florida posted a message to social media late Friday, saying Caitlyn Frisina was found safe in Syracuse.
The Columbia County Sheriff's Office said a deputy spotted their car, pulled them over and found both Frisina and Rian Rodriguez inside.
Frisina's family was notified and Rodriguez was taken into custody.
Frisina and Rodriguez might have been traveling north after the teen left her home on her own, leaving behind her phone, "which she fully erased," the Columbia County Sheriff's office said in a Facebook post on Sunday. Police said they found footprints outside of the teen's home, and she appears to have left through a window.
The teen was spotted at a pawn shop in South Carolina with a man believed to be Rodriquez.
Frisina's parents told police they had "no indicators" of "any type of relationship between these two," Murray Smith, public information officer for the Columbia County Sheriff's Office, told ABC News this week. From interviews, though, authorities said they have learned of what Smith described as the "blossoming of a potential relationship" between Frisina and Rodriguez.
"Caitlyn has a current boyfriend who also is beside himself because everything was fine," Smith said.
Her parents were begging her to come back home.
"We just want you to know we love you and miss you, we need to know you are safe," mom Scarlet Frisina said.
Rodriguez has been working as a boys' soccer coach at Fort White High School, but he has been suspended pending the investigation, according to a statement from Lex Carswell, superintendent of Columbia County Schools.
Frisina has played soccer at Fort White High School, according to an online roster published by Next College Student Athlete.
Rodriguez and Frisina had been around each other "at sports events, but they've never been alone at all," Smith said.
The sheriff's office said Frisina made a $200 ATM withdrawal Sunday in St. Marys, Georgia, which is about 100 miles northeast of Columbia County. That was the teen's last known location, Smith said.
He said Frisina has family in New York and Rodriguez has family in Canada and possibly Pennsylvania.