Although the United Food and Commercial Workers was certified as a bargaining agent in 2008, the two parties have never reached a collective bargaining agreement.
After a decertification drive was launched at the store and employees voted on that, the union argued the process was unfair and sought to block the votes from being counted.
But on Thursday, after the Supreme Court of Canada dismissed the union's application to deal with the case, the way was cleared for the count to be held.
The Saskatchewan Labour Relations Board still needs to decide if the results are binding.
The Weyburn decertification drive was the latest chapter in the fight between Wal-Mart and the union that's been going on for nine years.
Wal-Mart has long resisted unionization at its North American stores, and the Weyburn store is the only unionized Wal-Mart in Canada.
Two other Canadian Wal-Marts have been certified in the past: the store at St. Hyacinthe, Que., and a store at Jonquière, Que.
However, employees at the Hyacinthe outlet later voted to decertify, and Wal-Mart closed the Jonquière store.