But the typical finance director in the sector is worse off than a year ago, with the average salary not keeping pace with inflation.
The survey, from accountancy company Hays, found that the national average salary for a charity finance director was £47,400, a rise of just 0.6 per cent in the past 12 months.
The charity sector's financial elite - directors of corporate resources - earn between £57,000 and £143,000. Their responsibilities include not only finance matters, but also business development, human resources and IT.
The survey shows that in some cases their pay can rival or exceed that of charity chief executives. The top chief executive salary in Acevo's survey of 400 voluntary organisations in 2004 was £133,000, £10,000 less than the top wage in the Hays survey. According to Acevo, two out of 400 chief executives earn less than their finance chief.
The salaries of finance directors range between £30,000 and £125,000.
Finance staff earn the least in Northern Ireland, Wales and Scotland and are most handsomely rewarded in the north west of England and London.
The average salary for a finance director in London is £64,000 and £55,000 in the north west. Of the other English regions, the south east pays the best, with an average of £52,000, while the East Midlands is the least generous, with a typical salary of £46,000.
Rebecca Craddock, senior finance specialist in the not-for-profit division at Hays, said pay was lagging further behind in smaller organisations, while the largest London-based charities were offering above-inflation rises.
But Charles Nall, corporate services director at The Children's Society, said: "Salaries for roles fluctuate with supply and demand. Financial directors, as custodians of scarce resources, appreciate this better than most. While this year's rise may be weak, growing demand for financial expertise across the economy will see the wheel turn later on."
Craddock said charities had trouble attracting junior finance staff: "Newly qualified accountants can earn between £10,000 and £15,000 more in the commercial sector."