Kasia Kowalska-Trela, 41, from Salford claimed her daughter Oliwia, 14, was told to find another pair of shoes from the school's lost and found cupboard, or face detention if she didn't comply.
After recently paying £50 for the shoes, Kowalska-Trela was frustrated she had to buy a new pair.
"There is absolutely nothing wrong with them, but the school classes them as boots," she told Manchester Evening News.
"They’re half an inch higher than other shoes. It’s ridiculous."
Kowalska-Trela said her daughter used to wear Kickers shoes to school, which looked similar to her boots now, but the uniform policy changed "without anybody being told", to include a rule that students have to wear shoes that sit below the ankle.
She said with her daughter needed a sturdy pair of shoes because she has to walk 30 minutes to school every day.
"They’re very modest, plain, old school leather shoes. They’re not overly chunky," she said, according to ITV News.
Kowalska-Trela claims her daughter wore the shoes for two months before the school noticed.
However now they have been picked up and reportedly described as "inappropriate footwear".
The mother told The Sun: "Oliwia is such a hard-working and obedient student and the rest of her school uniform is always immaculate.
"The whole experience has been very stressful for her.”
HuffPost UK Parents has contacted the school for comment.
In September 2015, a similar story came to light when more than 50 pupils returning to school were sent home for wearing "unsuitable shoes".
Those not wearing plain black leather shoes were rounded up and taken to the sports hall before 56 were sent home to change.
Headteacher Dave Hooker, said: "Being appropriately dressed, whether for school or work, is a lesson that will benefit all our students throughout their lives."