Adventure Kokoda's commercial tour operator's licence was cancelled in April following a dispute involving trekking fees, legal documents show.
The company wanted to give fees directly to campsite owners so they could upgrade facilities to meet hygiene and safety concerns, instead of the local authority charged with managing the track.
However, the Kokoda Track Authority warned against it and said failure to pay would be considered breaking the law.
In April, the company's director Charlie Lynn embarked on a trek one day before fees for that trip were paid in full, according to court documents.
Adventure Kokoda's licence was cancelled by the end of that month.
PNG's minister for Environment, Conservation and Climate Change Simon Kilepa, who is also the chair of the Kokoda Initiative Committee, at the time described it as "deliberate and calculated actions to contravene PNG Law".
However, the company launched legal action and in late December the country's National Court quashed the licence cancellation.
Judge Susan Purdon-Sully said the decision to cancel the licence was invalid, ordered for it to be restored by the local authority and for defendants to pay all legal costs.
Charlie Lynn says he hopes the court decision will spark changes to how the Kokoda track is managed. (HANDOUT/CHARLIE LYNN)
Mr Lynn said he had always been confident the court would find in his favour but was still greatly relieved by the outcome.
"The company is now run by my son-in-law and my daughter, they've had a terrible time and lost a lot of business," Mr Lynn told AAP.
"So we can now get back and start to rebuild."
Mr Lynn is a Vietnam veteran and former NSW Liberal MP who has been leading Kokoda treks for three decades and was one of the first to walk it in 1992.
He hopes the decision will spark changes to how the track is operated and hopes to see improvements including battle sites being honoured.
"It has the potential to be a world-class pilgrimage tourism destination," Mr Lynn said.
The Kokoda Track Authority and the office of PNG's minister for environment, conservation and climate change have been approached for comment.
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