While some health boards refuse to fund the controversial style of treatment, others spend thousands of pounds every year and one area spent almost £10 million in five years, according to the statistics obtained by the Scottish Conservatives.
In five years, almost £12.3m was spent on homeopathic treatment in Scotland.
NHS Greater Glasgow and Clyde, which has a homeopathy hospital and also caters for patients from Ayrshire and Arran, has spent £9.7m since 2008/9. NHS Lothian, which announced in June this year that it was to "move away" from offering the treatment, has spent more than £1.1m on it over the same five-year period.
However, three health boards - Fife, Forth Valley and Lanarkshire - refuse to offer homeopathy and have spent nothing on it.
Scottish Conservative health spokesman and deputy leader, Jackson Carlaw MSP, said: "It doesn't really matter whether you think homeopathy is a lifesaver or a nonsense, this disparity has to end.
"We need a proper debate on the merits of the treatment so a proper approach can be taken."
A Scottish Government spokesman said: "Complementary and alternative medicine (CAM) therapy covers a wide range of services and we recognise that CAM therapies may offer relief to some people suffering from a wide variety of conditions."