The government wants to delay the over-the-counter sale of "Plan B" emergency contraception to girls of any age.
The Obama administration filed an eleventh-hour appeal on Monday.
Last month, U.S. District Judge Edward Korman ruled that the so-called "morning after" pill be made available without a prescription.
Korman denied a U.S. government request to put a hold on his order while the Obama administration readied an appeal on Friday.
The Food and Drug Administration lowered the age limit for access to the emergency contraceptive from 17 to 15 years of age, but Korman believes that doesn't go far enough.
In the appeal document, the government contends that Korman overstepped his authority.
The Center for Reproductive Rights plan to answer the Obama administration's filing within 10 days.