Healius was advised in 2015 that lump sum payments made by Healius to healthcare practitioners for the 2010 to 2014 financial years were tax deductible.
Healius subsequently filed an application for similar tax deductions for the financial years 2003 to 2007.
The Commissioner of Taxation did not allow Healius to lodge an out-of-time objection regarding the earlier taxation years.
The court win means that Healius can pursue a refund of tax payments and associated interest estimated at around $60 million.
Shares in Healius (ASX:HLS) are trading 1.9 per cent lower at $3.09.