Welwyn Hatfield and Potters Bar schools are staying in the black while a growing number spend beyond the funding they receive, according to the latest figures.
New data from the Department for Education shows four of 20 (20 per cent) local authority-run secondary schools in Hertfordshire, for which figures were available, finished the last financial year in deficit.
This means their budget was not enough to cover all costs in the 12 months to March.
However, of those 20, the two schools in Welwyn Hatfield recorded strong surpluses: Chancellor’s School in Brookmans Park (£320,470) and Ridgeway Academy, formerly Sir Frederic Osborn School, in Welwyn Garden City (£169,409).
Figures for the 2017-18 financial year for other secondary schools in the borough were not available.
Nationwide, more than 30 per cent of secondary schools are now spending more than their budget, up from 13% five years ago.
The figures exclude academies, which are government-funded but are not overseen by the local authority.
Dr Mary Bousted, joint general secretary at the National Education Union, said: “This debt is being incurred despite schools taking desperate measure to balance the books such as making thousands of teachers and teaching assistants redundant, increasing class sizes, cutting subject choices, and leaving essential building repairs undone.
“Yet still the Government does nothing about the woeful lack of funding given to our schools and colleges.”
Schools are normally required to balance their books, although councils can allow schools to go into the red in exceptional circumstances if the amount is swiftly paid back.
Eight primary schools of the 364 in Hertfordshire for which figures were available were in the red, but none of those eight are in Welwyn Hatfield.
Pope Paul Catholic Primary School in Potters Bar had a slim total revenue balance of £3,143 and Tewin Cowper C Of E VA Primary School in Welwyn had an unspent £20,742.
The strongest surpluses were Cuffley School near Potters Bar (£559,852), Swallow Dell Primary and Nursery School in Welwyn Garden City (£485,829), De Havilland Primary School in Hatfield (£412,645), Oak View Primary and Nursery School in Hatfield (£359,328) and Codicote C of E Primary School in Codicote (£314,276).
Figures were not available for some schools.
Jon Andrews, director for school system and performance at the think tank Education Policy Institute, said councils could help “ease pressure” on schools by recirculating some of the funds that others haven’t used.
However, schools should not be penalised for running a reasonable surplus, he added, which is the result of good financial management.
Overall, 3 per cent of all maintained nurseries, primary schools and secondary schools across Hertfordshire are now in the red. Schools in deficit overspent by about £2.8 million during the year to March - the equivalent of £213,100 each.
The Department for Education said it was giving more money to schools, and had allocated the biggest increases to the schools that have been most underfunded.
A spokeswoman said: “However, we know that we are asking schools to do more, which is why the Education Secretary has set out his determination to work with the sector to help schools reduce the £10 billion they spend on non-staffing costs and ensure every pound is spent as effectively as possible.”
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