A Scottish Premier League-appointed independent commission - chaired by Lord Nimmo Smith - imposed the fine after finding the Ibrox side guilty of failing to make proper disclosure of side-letter arrangements during 2000-2011.
However, the club avoided the most severe sanction of losing up to five SPL titles won during the period investigated after the commission ruled Rangers "did not gain any unfair competitive advantage".
The three-man commission, which also comprised QCs Nicholas Stewart and Charles Flint, were unanimous in their decision.
In full: the commission's report into Rangers use of EBTs
They found that Rangers, under Sir David Murray`s stewardship, entered into side-letter arrangements with a large number of players, with the club making payments to an offshore Employee Benefit Trust (EBT) and payments made to players in the form of loans.
The commission found that those arrangements - which were required to be disclosed under the rules of the SPL and the Scottish Football Association - were not disclosed to the football authorities.
The commission statement read: "Although the payments in this case were not themselves irregular and were not in breach of SPL or SFA Rules, the scale and extent of the proven contraventions of the disclosure rules require a substantial penalty to be imposed.
"Rangers FC did not gain any unfair competitive advantage from the contraventions of the SPL rules in failing to make proper disclosure of the side-letter arrangements, nor did the non-disclosure have the effect that any of the registered players were ineligible to play, and for this and other reasons no sporting sanction or penalty should be imposed upon Rangers FC."
The commision confirmed their earlier decision that newco Rangers could not be held responsible for any breach of rules by the oldco.
They added: "In all the circumstances the commission has imposed a fine of £250,000 on Oldco."
The EBT payments were the subject of a tax tribunal which oldco Rangers won in principle in November last year, although Her Majesty's Revenue and Customs have launched an appeal.
The commission concluded it was clear that the non-disclosure was "at least partly motivated by a wish not to risk prejudicing the tax advantages of the EBT scheme".
But they concluded no sporting advantage was gained, directly or indirectly, partly because of the tax tribunal's findings that the arrangements "did not give rise to payments absolutely or unreservedly held for or to the order of the individual players".
The statement added: "On that basis, the EBT arrangements could have been disclosed as contractual arrangements giving rise to a facility for the player to receive loans, and there would have been no breach of the disclosure rules."
However, the commission stated that the assumption that the undisclosed arrangements were discretionary and did not form part of any player's contractual entitlement, was "seriously misconceived".
And they took a serious view of a breach of rules intended to promote "sporting integrity" and "prevent financial irregularities", while noting the extent of the payments - more than £9million was paid to employees through EBTs in the 2005-06 season alone.
They also found no evidence that the Ibrox board had taken any expert advice as to whether disclosure would have affected their tax liability.
The commission said: "The directors of Oldco must bear a heavy responsibility for this. While there is no question of dishonesty, individual or corporate, we nevertheless take the view that the nondisclosure must be regarded as deliberate, in the sense that a decision was taken that the sideletters need not be or should not be disclosed.
"No steps were taken to check, even on a hypothetical basis, the validity of that assumption with the SPL or the SFA."
They added: "Given the seriousness, extent and duration of the non-disclosure, we have concluded that nothing less than a substantial financial penalty on Oldco will suffice.
"Although we are well aware that, as Oldco is in liquidation with an apparently massive deficiency for creditors (even leaving aside a possible reversal of the Tax Tribunal decision on appeal), in practice any fine is likely to be substantially irrecoverable and to the extent that it is recovered the cost will be borne by the creditors of Oldco, we nevertheless think it essential to mark the seriousness of the contraventions with a large financial penalty."
The decision is set to conclude a lengthy process begun by the SPL on March 5, before Rangers were consigned to liquidation and were relaunched as a new company.
Some of the delay was caused by administrators Duff and Phelps' failure to release documents, for which oldco Rangers were "admonished" today. The commission was appointed on August 2.
Charles Green's newco club refused to co-operate with the investigation, although the oldco club were represented at the hearing, which began on January 29, after submitting a statement days earlier.
Rangers EBT timeline
The titles Rangers faced losing
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