Amy Yu was located at a Mexican resort town on Saturday night, ABC News confirmed after speaking briefly with Yu's mom.
"I'm really happy. Please let everyone know," she told ABC News.
Yu arrived at Philadelphia International Airport early Sunday morning and was taken back home to Allentown.
Yu along with Kevin Esterly, 45, has been missing since March 5, and when the girl did not return home from school that night, her mother reported her missing, the Allentown Police Department said.
Amy was believed to have willingly accompanied Esterly out of the country on a one-way flight by way of Dallas, Texas.
The pair were together at the coastal destination Playa del Carmen, in the state of Quintana Roo, according to a U.S. Department of Homeland Security Investigations release.
Once authorities from the U.S. Marshals Service and Mexican federal investigators pinpointed the pair, according to the release, Esterly was placed into Mexican custody and they were flown to Miami, Florida.
Esterly has been turned over to Miami Police Department and is awaiting extradition to Allentown where he is facing a felony charge of custodial interference.
"HSI is happy that United States citizen, Amy Yu, a 16-year-old juvenile runaway, has been safely returned to Pennsylvania," said Marlon Miller, special agent in charge of the HSI Philadelphia.
Allentown Police Chief Glen Dorney stated, "Amy is unharmed and in good health" and that once Yu is back stateside she would be "reunited with her mother."
Authorities said he withdrew $4,000 from his wife Stacey's bank account and signed the youth out of the school--falsely claiming to be her stepfather.
The dragnet to recover Yu and apprehend Esterly was extensive.
It was capped by the Mexican government issuing a March 15 Amber Alert.
ABC News' Emily Shapiro contributed to this report.