Frank Ciccotti, headteacher, has consulted parents about the plans. And from September, half of the 240-strong Year 8 group will be taught in single-sex classes for English, maths, science, history and design technology - around half their weekly timetable.
Teachers are being asked to adjust their methods accordingly. Boys can expect more competitive, practical and time-limited activities and close monitoring of their presentation and completion of work. Girls are to be rewarded for participation in discussion and co-operative activities, and for taking risks academically.
The Women in Science and Engineering campaign (WISE) claims that girls develop more positive attitudes towards science subjects in single-sex lessons. And, without the boys hogging equipment and showing off during practicals, they gain confidence in hands-on work.
In guidance published earlier this year, WISE said some boys as well as girls preferred single-sex lessons.
In Pembrokeshire, the pass rate for five good GCSEs for both boys and girls is virtually the same as for Wales as a whole. The girls lead, though - by 58 to 46 per cent.
At Pembroke school last year, 33 per cent of girls and 38 per cent of boys got at least a grade C in maths, but in Wales as a whole, girls did better than boys by four percentage points. In science, the Pembroke boys were 13 percentage points ahead (41 to 28 per cent), compared to a two-point lead for the girls nationally.
"Historically there is an under-achievement by girls here. It is difficult to understand why," said Mr Ciccotti. "Other schools have found that by splitting classes into single-sex groups there have been marked improvements, particularly in science and maths.
"Initiatives in education can sound like good wheezes but this appears to have a sound basis."
The main concern is that splitting classes could create difficult groups of low-attaining boys. The school has previously experimented, unsuccessfully, with single-sex classes at GCSE and concluded that by 15 it was too late to make a difference. But Mr Ciccotti is confident the initiative will work if introduced earlier.