Coy Mathis's family had taken her and her four siblings out of the Eagleside Elementary school in Fountain while the case was ongoing.
The Colorado Civil Rights Division ruled on Sunday that the Fountain-Fort Carson School District had caused an unnecessarily hostile situation for Coy by not allowing her to use the girls' lavatories. Steven Chavez, the division director, said that the school had created 'an environment rife with harassment'.
Coy, who was born male but has identified as female since the age of four, had suddenly been banned from entering the girls' facilities at the school, despite having been recognised as a girl throughout her time at the school.
Her parents, Kathryn and Jeremy Mathis, filed a complaint through the Transgender Legal Defense and Education Fund in February after they received a call from the school telling them that when Coy returned from the winter break, she would have to use the boys' toilets.
"She would use the girls restrooms, she would be called a girl, she would go in the girls' lines," Kathryn Mathis told chat show host Katie Couric at the time.
"It came out that Coy was no longer going to be able to use the girlss restroom and they were going to require her to be using the boys' room, the staff bathroom or the bathroom for the sick children. We didn't know why, we had no idea where this was coming from.
"We got a call one evening, it was the principal and he said he wanted to set up a meeting with us to discuss options for Coy's future use of the restroom," added her husband, Jeremy.
The school's lawyer, W Kelly Dude, told reporters back in February that the decision had been made in order to protect all the school's students and 'took into account not only Coy but other students in the building, their parents, and the future impact a boy with male genitals using a girls' bathroom would have as Coy grew older'.
The Mail reports that the family's action was the first to challenge transgender people's access to bathrooms under Colorado's anti-discrimination laws.
Coy's delighted mum said that the family were pleased and relieved that she will now be treated the same as other girls in her school.
"Schools should not discriminate against their students, and we are thrilled that Coy can return to school and put this behind her," Kathryn said. "All we ever wanted was for Coy's school to treat her the same as other little girls. We are extremely happy that she now will be treated equally."