Fees applied to Visa card purchases "remain unacceptably high," the company said in a statement.
Customers will no longer be able to use the card in its Thunder Bay store from 18 July and the move will be phased in across the country.
Visa accused Walmart of putting its own financial interests ahead of its customers.
"Walmart made this business decision despite Visa offering one of the lowest rates available to any merchant in the country," a spokesperson said.
The supermarket chain said it paid more than $100m (Â£70m) in credit card fees each year - but did not break that down for the specific companies.
All credit cards charge fees to retailers - generally between 1% and 2.5% of the sale cost. Visa and Mastercard usually charge variable fees according to the type of card used, while American Express generally charges a flat fee.
"To ensure we are taking care of our customers' best interests and delivering on our promise of saving customers money, we constantly work to reduce our operating costs, including credit card fees," Walmart Canada said.
However the company added that it remained "optimistic that we will reach an agreement with Visa".
Walmart has some 370 stores in Canada.
Last month the company as a whole reported a 7.8% fall in profit for the first three months of the year to $3.08bn.
Retailer Walmart Canada will no longer accept Visa cards after it failed to agree a deal with the credit card firm.