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Furuta's intended future employer presented her parents with the uniform she would have worn in the position she had accepted. The uniform was placed in her casket. At her graduation, Furuta’s school principal presented her a high school diploma, which was given to her parents. The location near where Furuta's body was discovered has been developed since and is now Wakasu park.

Nobuharu Minato, who originally received a four-to-six-year sentence, was re-sentenced to five-to-nine years by Judge Ryūji Yanase upon appeal. He was 16 at the time of the murder. Minato's parents and brother were not charged. Furuta's parents were dismayed by the sentences received by their daughter's killers and won a civil suit against the parents of Nobuharu Minato, in whose home the crimes were committed. After his release, Minato moved in with his mother. He has not worked since. In 2018, Minato was arrested again for attempted murder after beating a 32-year old man with a metal rod and slashing his throat with a knife.

In November of 2017, an album titled Don't Be Afraid of Dying was released by musician Sewerslvt as a tribute to her death, with each letter at the start of each song spelling out her name.

Jun-chan, welcome back. I have never dreamed that we would see you again in this way. You must have been in so much pain ... so much suffering ... The happi we all made for the school festival looked really good on you. We will never forget you. I have heard that the headmaster has presented you with a graduation certificate. So we graduated together – all of us. Jun-chan, there is no more pain, no more suffering. Please rest in peace...

Miyano was denied parole in 2004. In January 2013, Miyano was re-arrested for fraud. Due to insufficient evidence, he was released without charge later that month.

Her murder was the inspiration for the film Concrete in 2004. In addition, the manga 17-sai. used the Furuta case as its basis.

For his participation in the crime, Jō Ogura served eight years in a juvenile prison before he was released in August 1999. He was 17 at the time of the murder. After his release, he is said to have boasted about his role in the kidnapping, rape and torture of Furuta. In July 2004, he was arrested for assaulting Takatoshi Isono, an acquaintance he thought his girlfriend may have been involved with. Ogura tracked Isono down, beat him, and shoved him into his truck. He drove him from Adachi to his mother's bar in Misato, where he allegedly beat Isono for four hours. During that time, Ogura repeatedly threatened to kill the man, telling him that he'd killed before and knew how to get away with it. He was sentenced to seven years in prison for the assault on Isono and has since been released. Ogura's mother allegedly vandalized Furuta's grave, stating that she had ruined her son's life. It has also been reported that Ogura had depleted his father's savings, money which was intended to be provided as restitution to Furuta's family, buying and consuming a number of luxury goods.

In July 1990, a lower court sentenced Hiroshi Miyano, the alleged leader of the crime, to 17 years in prison. He appealed his sentence, but Tokyo High Court judge Ryūji Yanase sentenced him to an additional three years in prison. The 20-year sentence is the second-highest sentence given in Japan before life imprisonment. He was 18 at the time of the murder. Miyano's mother reportedly sent Furuta's parents 50 million yen (US$425,000), after selling their family home.

On 4 January 1989, after losing a game of Mahjong, Hiroshi Miyano decided to vent his anger on Furuta. At this point, Furuta was barely alive. Out of frustration, the boys beat her with an iron barbell, kicked and punched her, and placed two short candles on her eyelids, burning them with the hot wax. They made her stand, and struck her feet with a stick. At this point, she fell onto a stereo unit and collapsed into a fit of convulsions. Since she was bleeding profusely, and pus was emerging from her infected burns, the four boys covered their hands in plastic bags, which were taped at the wrists. They continued to beat her and dropped an iron exercise ball onto her stomach several times. They poured lighter fluid onto her thighs, arms, face, and stomach and once again set her on fire. Furuta allegedly made attempts to put out the fire, but gradually became unresponsive. The attack reportedly lasted two hours. Furuta eventually succumbed to her wounds and died that day.

On 23 January 1989, Hiroshi Miyano and Jō Ogura were arrested for the gang-rape of the 19-year-old woman who they had kidnapped in December. On 29 March, two police officers came to interrogate them, as women's underwear had been found at their addresses. During the interrogation, one of the officers led Miyano into believing that police were aware of a murder committed by Miyano. Thinking that Jō Ogura had confessed to the crimes against Furuta, Miyano told the police where to find Furuta's body. The police were initially puzzled by the confession, as they had been referring to the murder of a different woman and her seven-year-old son that had occurred nine days prior to Furuta's abduction. That case remains unsolved to this day.

The police found the drum containing Furuta's body the following day. She was identified via fingerprints. On 1 April 1989, Jō Ogura was arrested for a separate sexual assault, and subsequently re-arrested for Furuta's murder. The arrest of Yasushi Watanabe, Nobuharu Minato, and Minato's brother followed.

Junko Furuta's funeral was held on 2 April 1989. One of her friends' memorial address stated:

On 25 November 1988, Miyano and his friend Nobuharu Minato wandered around Misato with the intention of robbing and raping local women. At 8:30 pm, they spotted Furuta cycling home after she finished her part-time job. Under Miyano's orders, Minato kicked Furuta off her bicycle and immediately fled the scene. Miyano, under the pretense of it being a coincidence that he had witnessed this attack, approached Furuta and offered to walk her home safely. Furuta, accepting this offer, was unaware that Miyano was leading her to a nearby warehouse, where he revealed his yakuza connections. Miyano threatened to kill her as he raped her in the warehouse and once again in a nearby hotel. From the hotel, Miyano called Minato and his other friends, Jō Ogura and Yasushi Watanabe, and bragged to them about the rape. Ogura reportedly asked Miyano to keep her in captivity in order to allow numerous people to sexually assault her. The group had a history of gang rape and had recently kidnapped and raped another girl who was released afterward.