Education minister Huw Lewis praised the work of staff and students involved in the Schools Challenge Cymru which he said was "delivering real and unprecedented improvements".
The Welsh government said early indications had shown that the majority of the 40 schools participating in the challenge had seen an increase in their GCSE results after just one year of additional support.
The participating schools are being collectively supported by up to £20 million of extra funding along with an individually tailored programme of support.
Of the 40 Challenge schools, around two thirds have reported an improvement in the number of their pupils gaining five or more A* to C GCSEs this summer.
And schools such as St Cenydd, Tonypandy and Pentrehafod have reported their best ever results. Blackwood Comprehensive reported improvements of more than 10 per cent.
Schools Challenge Cymru Champion, Professor Mel Ainscow, said: "We have seen some truly outstanding improvements from a number of schools participating in the Schools Challenge Cymru. We must remember that these are some of our most challenged schools from some of our most disadvantaged communities and to see this level of improvement after just one year of intervention really is something to celebrate.
"Well done to the pupils and their teachers. Results like this follow a great deal of hard work and commitment and we will be building on this success as we move into the second year of the programme."
The minister added: "These are some of our most challenged schools and to see some of them reporting percentage improvement in the double figures really is remarkable."
There was further praise for secondary schools in Wales at the start of term with new figures showing that attendance levels are at a record high. The figures for 2014 to 2015 show overall absence is at its lowest ever recorded level. The government figures show 6.2 per cent of half-day school sessions were missed due to overall absence and 1.3 per cent of half-day school sessions were missed due to unauthorised absence from maintained secondary, special and independent schools.
The percentage of persistent absentees in maintained secondary schools has decreased every year since 2007/08. It is now less than half what it was seven years ago, showing a drop of 5.5 percentage points from 10 per cent in 2007/08 to 4.5 per cent in 2014/15.
The minister congratulated pupils and teachers across Wales for their "continued effort and commitment" adding: "We know school standards are rising across the board in Wales and we are committed to ensuring young people are given every opportunity to fulfil their potential. Regular attendance at school goes a long way towards achieving this."