As children, Junko and her twin sister Mukuro had lived in abject conditions and they were even homeless at some point. As she puts it, she regretted the moment of her own birth, feeling that her birth into the world was a mistake. Due to her analytical skills allowing her to predict the outcome of events, she became bored with the world. Because of that, she took an interest in despair, which she believes is unpredictable and exciting, at a very young age.
As a child, she was close with Yasuke Matsuda, as they didn't have any other friends. One particular moment between the two when they were elementary school students was when Junko spent a month building a sand sculpture modeled after the Sagrada Familia church at the public park, and she even used very advanced techniques for her age. The sculpture got closer to completion and many people from around the neighborhood came over just to watch her work.
One day, the sandcastle was found destroyed just before it was completed. Junko cried continuously for almost an entire day and Yasuke went around angrily looking for the perpetrator. Not being able to find out anything useful discouraged Yasuke. While he was sitting on a bench in front of the remains of the sand sculpture, Junko ran up to him with a large smile and whispered in his ear that she was the culprit who destroyed the sculpture all along, asking him to keep it a secret. When asked for a reason, she replied that she did so by accident. Truthfully, she had done this to get Yasuke out of his house, upset that his mother's condition had led him to become more withdrawn than usual.
In the years following the death of Yasuke's mother, Junko became the person that Yasuke felt he could always lean on. She promised to always be there for him, which helped develop his stronger feelings towards her. She said she'll never forget Yasuke even if she forgets everything else, and they'll always be together. For the first time in his life, Yasuke cried in front of another person, after making her promise she won't make fun of him, won't tell anyone and won't try to console him. Junko had romantic feelings for Yasuke, referring to them as "lovers", though Yasuke denied this.
Junko had a strong desire to "paint the world in despair" and planned to start The Tragedy, the worst, most despair-inducing incident in the history of mankind. She called herself and her sister the Despair Sisters AKA the Ultimate Despair.
As a teen, Junko began a modeling career and quickly became an idol amongst the Japanese population with her extravagant tastes. One reason for her popularity was the fact that, ironically, she didn't seem fake. Her career created a lot of unwanted attention as well; she claimed that the only men who were interested in her were "creeps who did not actually care about her."
Junko used to attend Gunma Prefectural Shibutani High School. She was scouted into Hope's Peak Academy as the Ultimate Fashionista along with her twin sister Mukuro, the Ultimate Soldier, into Class 78th. Unlike other students, her admission is a special case by the recommendation of the Steering Committee; her talent is guaranteed by the Committee, with explicit dis-involvement of Jin Kirigiri and Koichi Kizakura. The responsibility of her as a student was placed upon the headmaster after her admission, with the Committee removing their responsibility on her development.