The club secured the central defender as an 18-year-old, with the teenager Moyes’s final signing prior to his appointment at Manchester United.
Reports at the time claimed that Everton paid around £3m for Stones, but Moyes told Goals on Sunday that the fee was less than half that.
“I laugh when people say we paid £3m for John Stones, it was £1.25m," he said.
"It was in the January and the last signing of the window. We were trying to bring a striker in that we needed but we didn’t have the money.”
Stones has since become a reported target for numerous elite clubs, including Chelsea, Barcelona and Manchester United, with the Blues offering to pay around £40m for the 21-year-old last summer, and Barnsley have rubbished Moyes’s claims, insisting that he played “no part” in negotiations over the defender’s transfer.
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“The amount paid by Everton to Barnsley is Commercial in Confidence, and we would have expected that David Moyes would be bound by that obligation of confidentiality to his former employer,” a club statement read.
“However, given the categoric nature of the assertion made, it is incumbent on Barnsley FC to correct such a statement when it is markedly and unequivocally wrong and yet is made by someone that the public might think is authoritative on the subject.
“This is particularly the case since he has cited the same erroneous fee on previous occasions also.
“David Moyes played no part in any negotiation with Barnsley FC concerning the transfer of John Stones, which may explain why he is mistaken as to the fee paid.”