The couple's parents then took their case to a religious court which overruled KUA. On Monday, the pair finally wed.
According to the bride, she plans to pursue her education before thinking about having children.
Her 15 year-old husband, who has already dropped out of school, said he would continue working to feed his family.
While not the norm, early marriages take place throughout Indonesia.
According to the UN's children office Unicef, 14% of women in Indonesia are married before they turn 18 and 1% are married before they are 15.
The young couple's case sparked opposition from citizens, religious scholars and garnered a lot attention on social media.
President Joko Widodo has now said he plans to introduce new regulations to stop the practice of child marriage by raising the minimum age.
Lies Marcoes, an expert on gender and Islamic studies, told BBC Indonesia: "The state must recognise this very serious crisis - early marriage is a silent death alarm because it contributes to the high maternal mortality."
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