The 17-year-old went to a police station in the town of Aizuwakamatsu, north of Tokyo, carrying the head in a sports bag, Japanese media said.
The beheaded body of a woman was later found at the boy's home, police said.
This is the latest in a series of grisly killings in Japan, a country renowned for its low crime rate.
On Monday a severed human leg was discovered in a small river in central Tokyo.
In January, a 32-year-old woman was arrested after she confessed to killing her husband, dismembering him with a saw and dumping body parts around Tokyo.
'It's horrifying'
In the latest case, the boy, said to be a local high school student, reportedly told police he killed his mother with a knife during the night as she slept, and had acted alone.
Japanese press said the boy lived with his young brother, separately from their parents. Their mother was believed to have been visiting them on Monday.
The teenager was reported to have undergone psychiatric treatment at some point in the past.
Chief Cabinet Secretary Yasuhisa Shiozaki expressed his alarm at the reports. "If it's true, it's horrifying," he said.
Aizuwakamatsu is located in Fukushima prefecture, some 200km (125 miles) north of Tokyo.
Map highlighting the Fukushima prefecture. A boy from Aizuwakamatsu, Japan a town just north of Tokyo, walked into the local police station with a sports bag which police say contained the severed head of his mother.

"If it's true, then it is horrendous," said Cabinet Secretary Yasuhisa Shiozaki, the head spokesman for the Japanese government.

Police say the 17-year-old boy told them that he killed his mother Monday night, and that he acted alone. Police later found the mother's remains inside the boy's apartment. Police say that an object much like a knife was used to sever her head.

There have been a series of murders involving the dismemberment of body parts in Japan in the past few months. A leg severed from an unknown body was found in Tokyo inside a trash bin on Monday. A woman, 32, was arrested in January when she admitted to murdering her husband, dismembering his body, then placed his remains around several spots in Tokyo.