Lawyers with the Justice Department filed the appeal with the 2nd US Circuit Court of Appeals in New York, according to court documents.
The appeal is the latest foray in the years-long legal battle over the pill known as "Plan B," a drug that has also sparked political and religious clashes. If taken up to 120 hours after unprotected sex, it is designed to prevent pregnancy.
The government is seeking to overturn US District Judge Edward Korman's ruling from April 5 that required the FDA to make the emergency contraception available over-the-counter to women of all ages within 30 days.
The Justice Department has asked the district court to temporarily stop its order from taking effect while the appeal is pending, said FDA spokeswoman Erica Jefferson.
The district judge's ruling came in response to a lawsuit originally filed in 2005 by the Center for Reproductive Rights and other groups seeking to strike down age and access limits to the emergency contraception. They argued that there was no scientific proof that girls of reproductive age could not safely use the drug without supervision.
Korman's order reversed a surprise December 2011 decision by US Health and Human Services Secretary Kathleen Sebelius. At the time, the FDA had decided to approve over-the-counter sales with no age limits when Sebelius ordered it to reverse course, barring girls under 17 from buying the pills without a prescription.
President Barack Obama supported that restriction, invoking his daughters. But the timing, 11 months ahead of the presidential election, sparked criticism that he was trying to placate social conservatives.
In his ruling, Korman called Sebelius' decision "arbitrary, capricious and unreasonable."
"The motivation for the secretary's action was obviously political," he wrote.
Nancy Northup, president of the Center for Reproductive Rights, criticized the government's decision to appeal.
Obama's "administration has decided once again to deprive women of their right to obtain emergency contraception without unjustified and burdensome restrictions," she said in a statement.
Before filing its appeal, the FDA said on Tuesday that it would allow girls as young as 15 years old to buy without a prescription the Plan B One-Step emergency contraceptive, made by a unit of Teva Pharmaceutical Industries Ltd.
The agency said its decision to lower the age limit for Plan B One-Step was based on scientific data submitted by Teva that showed girls as young as 15 could safely use the drug without the intervention of a healthcare provider.
Cashiers will still have to verify the customer's age before selling it, the FDA said.
The case is Tummino et al. v. Hamburg et al., US District Court for the Eastern District of New York, No. 12-763.