Girls from Walkwood Church of England Middle School in Redditch, Worcestershire, have been told to wear trousers from September amid concerns over shrinking hemlines.
The school will also ban female pupils from donning blouses from 2014 to ensure boys and girls wear the same uniform, The Telegraph reported.
But the move has been branded "crazy" by parents who warned that denying young girls the chance to wear skirts would leave them confused.
One campaign group said 63 schools currently banned children from wearing skirts. Most are secondaries but at least one other middle school, teaching nine- to 13-year-olds- have launched a similar crackdown.
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"Some of the older girls were beginning to wear extremely short skirts. It was becoming difficult, especially when it came to them sitting down in the school hall. It was very unladylike," Doubtfire was quoted by the daily as saying.
"We would ask them to make their skirts longer, but they would just roll them up again when we turned away. We want to simplify the uniform. It was getting complicated and this should make it cheaper for parents. Some of the blouses were expensive," he said.
Walkwood, which is currently rated as "satisfactory" by Ofsted, teaches 723 boys and girls aged nine to 13.
A group of 20 parents have now written to the school to complain over the skirt ban.
One parent, who did not want to be named, said: "You hear so much about the over sexualisation of children these days but to call a nine-year-old girl unladylike is absurd".
"They aren't ladies, they are young girls. And to stop them from wearing skirts is just going to confuse them. I've always been against skirt bans, but I understand there has to be a limit for teenagers as they are turning into young women," the parent said.
The move comes after a group of boys from a secondary school in Cardiff launched a campaign earlier this month against teachers' refusal to allow them to wear shorts during the heatwave.
The Year 10 boys at Whitchurch High School turned up dressed in skirts at protest over the ban.