The head teacher of St Aidan's Church of England High School in Harrogate, North Yorkshire imposed a complete ban on skirts because young girls were "placing themselves at risk" by raising their hemlines.
From the start of the September term, all female pupils up to the age of 15 will have to wear long black trousers.
In a letter to parents at the mixed-sex school, Dennis Richards said that the strict new uniform rules were necessary because young children were "wholly unaware of the signals they are giving out" by wearing short skirts.
He said that earlier attempts to impose a minimum skirt length had led to "battles within the family home and unnecessary and time wasting confrontation at school", making a blanket ban the only effective solution.
The head teacher wrote: "We have been seriously concerned now, for a number of years, that girls as young as 12/13 years of age are placing themselves at risk by wearing skirts of a wholly inappropriate length.
"We are also aware that parents are becoming increasingly frustrated that the school seems incapable of imposing its authority on such young children. In the end we could probably do so but the cost in terms of detentions and exclusions would be very high and disproportionate to the end we would achieve."
In a statement on the school website he added: "Parents who have come in have been astonished to see the difference between the length their daughter may wear her skirt as she leaves home and what has happened by the time she is walking the corridors of the school."
Addressing sceptical parents, Mr Richards said: "The world has moved on. It is bizarre in 2010 to see wearing trousers as 'some form of punishment'."
While Mr Richards claimed to have received supportive messages from parents, the school has been criticised for failing to enforce its previous rules outlawing only shorter skirts.
Margaret Morrissey of the pressure group ParentsOutloud said: "Skirts of a reasonable length have a place in any school uniform.
"If a school can't get its pupils to abide by the rules there is a problem there. It sends out completely the wrong message to children if their misbehaviour leads to a change in the rules."
North Yorkshire County Council, the local authority with responsibility for education, said it did not comment on specific uniform policies.
But a spokeswoman said: "Decisions about school uniform are taken in the best interests of children by school leaders and governing bodies often in consultation with parents."
The skirt ban at St Aidan's covers pupils in Years 7 to 10. As part of the new uniform policy, girls in Year 11, who are aged 15 and 16, will be allowed to wear dark navy skirts so long as they are no more than three inches above the knee.
St Aidan's is a specialist science school with 1,898 pupils. It was praised as "an outstanding school in all respects" by Ofsted in 2006.
Other schools across the country are also tightening their uniform rules for the new academic year; Chipping Camden School in Gloucestershire has students from wearing hoodies, short skirts, denim and crop-tops.
--By Matthew Moore,14 Jun 2010