Schools in Sheffield, Doncaster and Barnsley have all performed worse than the national average for GCSE pass rates in state schools.
Rotherham was the only local authority area in South Yorkshire to perform better than the national average of 56.6 per cent of pupils achieving at least five GCSEs including Maths and English at grade C or above.
But its average for 2014 was 57.3 per cent - down on the 63.6 per cent success rate recorded in 2013.
Karen Borthwick, Head of the School Effectiveness Service for Rotherham Borough Council, said it was gratifying to see Rotherham’s students are doing well.
She said: “Although the Key Stage 4 performance measures cannot be compared with previous years because of the major reforms introduced by the Government in 2013, it is still great to see that our GCSE students are doing so well.
“Rotherham is the only authority in South Yorkshire to achieve overall results above the national average pass rate of 56.6 per cent. Its 57.3 per cent pass rate is a celebration of the achievement of all young people in Rotherham and the continued success of Rotherham schools.”
In Sheffield, the average success rate was 53.9 per cent, while in Doncaster and Barnsley less than half of the children taking GCSEs reached the five A* to Cs target.
In Doncaster, the average number of children hitting the target was 49.4 per cent, while in Barnsley it was just 47.1 per cent - the eighth-worst in the country.
The results come as teaching unions and politicians raised concerns about changes to way results are calculated.
The number of secondary schools considered to be under-performing has doubled in the wake of a major overhaul of the exams system, official figures show.
More than 300 schools fell beneath the Government’s floor target this year after failing to ensure that enough pupils gained five good GCSE grades and made decent progress in the basics, according to an analysis of new league tables.
The Department for Education insisted that the rise is down to two key reforms - a decision that only a teenager’s first attempt at a GCSE would count in the annual performance tables, and a move to strip poor quality vocational qualifications out of the rankings.
Clive Betts, MP for Sheffield South, said despite the difficulties, local schools must still aspire to improve, as the city’s latest results showed it was below the national average for children achieving five grade Cs or above.
“It is a long-term problem and it is not something new. It is a major challenge for our city. We want to be at the average or better,” he said.
Dr Mary Bousted, general secretary of the Association of Teachers and Lecturers, said: “Performance tables are too crude a measure of how well a school or college performs and with such major reforms to the exams system over the last year, it is impossible to compare results from previous years.
“The fall in GCSE grades is due, in part, to counting only the first GCSE grade rather than the best grade, plus changes to the way that vocational qualifications were counted. The Government insists on moving the goalposts year-on-year.”
The DfE said the two major changes to the exams system - which schools were told about around 18 months ago - do not affect pupils individual exam results.
Education Secretary Nicky Morgan said: “For too long pupils were offered courses of no value to them and schools felt pressured to enter young people for exams before they were ready.
“By stripping out thousands of poor quality qualifications and removing resits from tables some schools have seen changes in their standings.
“But fundamentally young people’s achievement matters more than being able to trumpet ever higher grades. Now pupils are spending more time in the classroom, not constantly sitting exams, and 90,000 more children are taking core academic subjects that will help them succeed in work and further study.”