David Fann, head of Sherwood Primary in Preston, Lancashire, said his local authority contacted him a few days before the Christmas holiday to say that his school would need to pay pound;16,500.
Mr Fann feared he would have to make redundancies because the extra bill pushed the school about pound;22,000 into the red. Instead, he took on the headship of the nearby Broughton CofE Primary, which did not have budgetary difficulties.
By getting each school to pay him for half the working week, he was able to save Sherwood Primary half his salary and solve its financial problems.
Mr Fann said some of the parents at Sherwood had been anxious when he began working at the other school.
"I have had to explain that it was because of the budget, which affects their children," he said.
Combining the two roles has meant working several 14-hour days at both schools for Mr Fann.
However, he said he had enjoyed the experience and would miss Broughton when its full-time head started in September.
Mr Fann said he felt support staff deserved the back pay, which was the result of legal challenges against local authorities across England. But he was angry that Lancashire county council had not warned him about the unexpected bill.
He was aware of another head who had received a larger bill, and feared that schools in other authorities would struggle.
The NAHT conference called for a review of the three-year school funding settlement in view of the state of the global economy and rising fuel costs.
Glyn Barker, a retired head from East Yorkshire, said schools would be left with no option but to cut staff.
"The true cost will be borne by the current generation of children," he said.
Jim Stead, a retired head, called on the Government to bail out schools that were in financial difficulties. "They did it for Northern Rock; they should do it for schools," he said.