In a letter to parents, Plymstock School in Devon says although "some girls leave their homes with their skirts at a reasonable length", they "roll them up for school".
From September, all students will have to wear dark grey trousers.
The letter said "time wasted addressing skirt issues would be better spent focusing on teaching and learning".
The school and Plymouth City Council were unavailable to comment.
One mother, who did not want to be named, said: "I've heard it's a small number of girls who have caused this, so the minority are spoiling it for everyone else.
"My daughter has a right to wear a skirt. Now she's worried she's going to be bullied in trousers."
Another mother, whose daughter is due to start at Plymstock in September, said she was so upset she had asked another school to take her daughter, but they were full.
The woman, who also did not want to be named, said: "She's really disappointed. I don't feel the school did enough to consult with parents."
The letter said: "Recent fashions have led to girls wearing skirts that are too short to be acceptable in the workplace.
"I am sure that some girls leave their homes with their skirts at a reasonable length but 'roll them up' for school," the letter said.
In 2014, the school attempted to tackle the issue of short skirts by placing "warning stickers" in the planning diaries of those pupils who had worn skirts "deemed too short".
"This will be the only warning and should they be found wearing an unacceptable skirt again they will forfeit their right to wear a skirt to school and will be required to wear trousers," a letter to parents at the time stated.
In 2011, Guiseley School in Leeds announced it was banning girls from wearing skirts after guidance on the length was ignored and the year before St Aidan's Church of England School in Harrogate also took the same action.
A school has completely banned pupils from wearing skirts because they have become too short.