Instead, from September, students at Moulton School and Science College in Northamptonshire will be forced to wear black tailored trousers.
Head teacher Trevor Jones said he has taken the radical decision in order to fight the "over-sexualisation" of children.
If they fail to obey the new rule, pupils will be given second-hand clothing to wear for the day or sent home to get changed, the Daily Mail reported.
Jones said he had seen girls coming into school with skirts halfway up their thighs or even higher.
"Some of them would be more appropriate in a nightclub than in a classroom. I think there is massive pressure with girls and image," he said.
"School should be a place where they can come and not have to worry about that for a few hours and instead concentrate on their learning," he added.
The existing rules had outlined that girls must wear skirts that were knee-length or below, but he said that this rule had been consistently broken.
"The minimum length was proving impossible to enforce, so we are now looking at a total ban. I have had complaints from a number of parents and some girls are feeling aggrieved but we think this will make the school a safer place," he said.
"It is another aspect of body image they don't have to worry about while they are here," he added.
The school's website states the rule change, saying: "School uniform plays a valuable role in contributing to the ethos of a school and setting an appropriate tone."
"It can instill pride, support positive behaviour and discipline, encourage identity with the school ethos and protect children from social pressures to dress in a particular way," it added.
It states that anyone not wearing the correct uniform will be offered second-hand clothing if available or children will be collected by their parents so they can return when correctly dressed.
The new uniform policy at the school also includes a ban on scarves and hats, unless in cold weather.
Trousers are not allowed to have any non-black stitching or visible metal buttons.
Moulton School and Science College is for boys and girls aged 11 to 18 and has around 1,300 pupils.