Last month, an upper-tier tax tribunal dismissed an HMRC appeal against a first-tier decision on payments made to players and other employees.
The tax authority argued unsuccessfully that the payments should be taxable.
The Murray Group, which formerly owned Rangers, argued that the payments were loans.
In a statement on Thursday, HMRC said it had applied for permission to appeal against the case to the Court of Session. It must prove there is a basis for the appeal on a point of law.
It said: "HMRC continues to believe that schemes using employee benefit trusts to avoid tax do not work.
"Around 700 users of EBT schemes have already settled with us resulting in around Â£800m 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."
The statement added: "HMRC is proud of our record of winning around 80% 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."
The first-tier tribunal (FTT) had issued a 2-1 majority verdict in November 2012 which favoured, in principle, the Murray Group and ordered that HMRC's Â£46.2m demands, about three-quarters of which referred to the liquidated club, be "reduced substantially".
The upper-tier appeal largely upheld that verdict but some payments will be re-examined by the original tribunal, including termination and "guaranteed bonus" payments.
The tax case has no impact on the current Rangers owners.
The Murray Group was unavailable for comment.
HM Revenue and Customs has announced it has applied for permission to appeal against a tax ruling over Rangers' use of employee benefit trusts (EBTs).