One in four West Midlands secondary schools went over budget last year.
The study, published by the Education Policy Institute (EPI), means they spent more than they received in funding.
And campaigners said schools will be forced to cut staff as they struggle to balance the books.
Geoff Barton, general secretary of the Association of School and College Leaders, said: “Staffing cuts are not just likely in the future, as the EPI report suggests, but have already taken place in many schools.
A study of school balance sheets shows that 24.6 per cent of West Midlands secondary schools, very nearly a quarter, ran up deficits in the 2016-17 financial year.
This was up from 11.9 per cent in the previous year.
It also found that 7.1 per cent of West Midlands primary schools, one in 14, went over budget.
That figure was up from 3.9 per cent the previous year.
The National Audit Office, an independent spending watchdog, last year warned that schools across the country needed to make savings of £3 billion to balance the books.
The Department for Education insists that schools have more money than ever before.
However, headteachers say that their costs have increased by even more.
David Laws, EPI executive chairman and former Lib Dem schools minister, said: “This analysis highlights the nature and scale of cost pressures facing England’s schools.
"After 15 years in which school funding has either been growing healthily or has at least been protected from inflationary pressures, school budgets are clearly now being squeezed.
“This is evident from the sharp rise in the number and proportion of local authority schools which are in budget deficit. The trebling of the proportion of maintained secondary schools over recent years is particularly striking.
“Many schools will need to find savings and it will not be easy to do this without reducing staff numbers.
"Schools and the Education Department will need to work hard to ensure that reduced staff numbers do not impact on education standards.”
Geoff Barton, general secretary of the Association of School and College Leaders, said: “This report shows that many schools are so cash-strapped they are unable to afford even a meagre pay rise of 1% for their staff next year without having to make further cuts.
“The Government has failed to provide schools with funding for pay awards over the course of several years, and this is one of a series of additional cost pressures which have pushed school finances to breaking point.
"Staffing cuts are not just likely in the future, as the EPI report suggests, but have already taken place in many schools.
“If the Government values education, it must put its money where its mouth is and provide schools with the funding they need to give all of our young people the very best start in life, and it must fully fund decent pay awards for school staff after years of austerity.”
A Department for Education spokesman said: “We do not recognise these findings. The fact is, thanks to our reforms and the hard work of teachers, standards are rising in our schools.
“By 2020, core school funding will rise to a record £43.5 billion - the IFS (Institute for Fiscal Studies) has confirmed that by then per pupil funding will have increased more than 70% since 1990.
“Latest figures show schools hold surpluses of more than £4 billion and we are providing support to help them get the most out of every pound they spend.”
Separate figures last week showed that Birmingham needs nearly 12,000 extra school places by September 2021, with 5,000 potentially needed by this September.
Figures released by the Department for Education show that, based on school capacity surveys as at May 2017, the local authority needs an estimated 4,689 extra school places by this September, and 11,918 extra by September 2021.
Across the West Midlands combined authority area, 18,479 extra school places are needed by September 2021, with 7,409 needed by September.