Frank Tall, a math professor at the University of Toronto, is using the Charter of Rights and Freedoms to challenge the act in Tax Court.
"I think taxpayers should be offered a choice as to what kind of medicine they want rather than only having one kind tax-deductible," he told CBC News.
Tall spends about $5,000 a year on homeopathic treatments, including vitamins and herbal remedies. He has been trying to claim a medical deduction since filing his 2001 tax return, but the claim has always been rejected.
He said that breaches the equality section of the charter.
"We contend that it constitutes religious and ethnic discrimination," he said.
Tall cites the Buddhist belief that "illness is caused by getting out of harmony with nature and is cured by restoring that harmony."
His argument has the support of the Canadian-Chinese National Council, which is making an application in court Monday to take part in Tall's challenge.
The organization's lawyer, Avvy Go, says traditional Chinese medicine should also qualify for a deduction.
"The choice of medical system ... [is] very much rooted in one's cultural and one's religion," Go said. "We often say, 'We're a multicultural society, we respect diversity, we respect the rights of individuals to choose ....'"
Canada Revenue Agency spokesman Sam Papadopoulos says he can't comment on specific cases, but he said the agency reviews the list of eligible medical expenses every year.
"If the medical community puts forward some new treatment, then we will add it to [the list]," Papadopoulos said.
"If those medicines are dispensed by a pharmacist, yes," they're deductible, he said. "If they're picked off the shelf, no."