Scottish judge Lord Doherty last month upheld a first-tier tribunal’s ruling in favour of oldco Rangers and former owners Murray International Holdings following an upper tier tribunal.
The case centres on the club’s use of the now outlawed Employee Benefit Trusts between 2001 and 2010.
More than £36million of payments were made to players and other employees, but the tribunal ruled they were rightfully classed as loans and therefore not subject to tax, a decision still disputed by HMRC.
A spokesperson from the tax authority said in a statement: “HMRC continues to believe that schemes using Employee Benefit Trusts to avoid tax do not work. We have applied for permission to appeal the case to the Court of Session.
“Around 700 users of EBT schemes have already settled with us resulting in around £800million of tax and NICs (National Insurance contributions) being paid. We expect more to settle in the near future.
“These are avoidance schemes and we will continue to tackle those who do not pay up. It is not right that a small minority can avoid paying what they owe while the vast majority pay the right tax on their earnings. This case represents an important principle.
“HMRC is proud of our record of winning around 80 per cent of cases that are taken to litigation by the taxpayer.
“We tackle avoidance wherever we see it and litigate where necessary to ensure schemes are defeated and the tax due is paid.”
Oldco Rangers went into administration, and ultimately liquidation, in 2012 over a separate tax debt which eventually reached £21million.
The ongoing legal battle does not affect the current Rangers regime.