The girl had previously been granted a much-sought-after spot at the Grenadjär School in Örebro in central Sweden, a publicly-funded, privately-managed free school with a Christian profile.
However, when staff discovered she had a pierced nose, the family was told she wasn't welcome.
"When we were going to sign the papers the principal said my daughter wasn't welcome in their school if she had a piercing in her nose," the mother wrote in her complaint to the Swedish Schools Inspectorate (Skolinspektionen), according to the Svenska Dagbladet (SvD) newspaper.
"She compared it to tattoos and short skirts."
According to the school's dress code, students aren't allowed to tattoos, clothing with racist slogans, or piercings.
School principal Yvonne Wirhall said the school's ban on piercings and tattoos is reasonable considering all the students are 15-years-old or younger.
"Our wish is that the girl leave the piercing at home," she told the local Nerikes Allehanda newspaper.
"That's something you do when you get older," she said.
Wirhall emphasised that the girl hasn't been denied entry to the school, per se, but that the school has expressed its desire that the small pearl the girl wears in her nose be left at home.
The request didn't sit well with the girl's mother, however, who chose report the school's policy to Sweden's education watchdog agency.
The agency, which received the complaint on June 10th, has requested that the school provide a response by July 7th.
According to Wirhall, she is prepared to change the school's policy if the agency finds that the school's ban on piercings is unjustified.