Portsmouth, owned by Saudi businessman Ali al Faraj, argued that the Value Added Tax (VAT) portion of its outstanding tax bill was too high by 7.5 million pounds.
A spokesperson for the Judicial Communications Office said: "At the High Court today Mr Justice Newey dismissed an application from Portsmouth Football Club Limited for a winding up petition to be struck out.
"A further hearing to consider HMRC's winding up petition will take place in due course."
The winding up order was issued by the Government's Revenue and Customs tax office.
However, in a statement, the club's solicitors Neumans LLP pointed out that despite his ruling, the judge commented that he found the issues in the case "difficult" and granted the club permission for appeal.
Neumans said that this meant the judge considered any appeal to the Court of Appeal would have "a real prospect of success."
Neumans added that if the appeal were to succeed "this would result in the judge's ruling being reversed and HMRC's petition being struck out, without the petition proceeding to a final hearing."
