They stated: "The majority view reflects the argument that the controversial monies received by the employees were not paid to them as their absolute entitlement. Thus the payments are loans, not earnings."
HMRC said at the time it was "disappointed" with the decision and a spokesman added: "We have lodged our appeal on the Rangers EBT case."
Rangers was under the control of Sir David Murray when it began using EBTs. He sold the club for £1 to Craig Whyte in 2011, while the tax liability was in dispute. The old club went into administration in February last year, owing up to £134 million to unsecured creditors.
The decision came too late to save "oldco" Rangers from being wound up and does not directly affect the current Ibrox regime.
The club was relaunched as a new corporate entity in June when the original company was consigned to liquidation.