The 15-year-old was arrested on Sunday in Sasebo city in Japan's southern Nagasaki prefecture.
Police said the girl beat her friend and then strangled her on Saturday. She then severed the victim's head and cut off one of her hands, they said.
The victim has been identified as a 15-year-old girl who attended the same high school as the suspect.
Her body was found in the apartment of the suspect, who was living apart from her parents, according to Japanese media reports.
Police said the suspect used a metal instrument to beat her friend.
They quoted the suspect as saying she acted alone, saying: "I did it all by myself", Kyodo news agency reported.
Ten years ago, a similar crime rocked the same city when an 11-year-old schoolgirl stabbed her 12-year-old friend to death.
In that case, the young girl told local media she acted because the victim had made comments about her appearance in internet chat-rooms.