The figures, which were revealed through Freedom of Information claims by the Scottish Conservatives, show only a single board, Orkney, has no outstanding claims.
With 141 cases resolved over the last four years, there are 9978 still outstanding. The settled cases have cost £586,475, making an average of £4100.
On that basis Greater Glasgow and Clyde could face a backlog worth some £17m while the bill in Lothian would be £6.7m.
Scottish Conservative local government spokeswoman Margaret Mitchell said: "This situation is clearly not sustainable – how can NHS boards be expected to plan for the future with this bill of millions of pounds hanging over them?
"Where there is a case to be resolved, it should be done so promptly and efficiently – the only people who will benefit by it dragging on are lawyers. Instead of spending millions kicking this into the long grass, NHS boards should be facing up to these claims."
Scottish Labour's Jackie Baillie said: "It is a disgrace that in 21st-century Scotland, women still are having to fight to achieve equal pay in the public sector.
"What is also more worrying is the financial time bomb that these claims pose for the NHS and the taxpayer."