Boyle, 37, will become an unrestricted free agent July 1.
Wilson also informed right wing Martin Havlat that "he will not be back this next season."
Havlat, 33, has one-year left on his contract and is expected to be bought out next month.
The Sharks have two compliance buyouts and will presumably use one of them on Havlat when the buyout period begins.
Wilson also revealed that defenseman-turned-forward Brent Burns will return to his natural position on the blueline next season.
With Boyle not returning and Havlat to be bought out, the Sharks will have roughly $15 million to $18 million in available salary cap space next season, depending on where the cap ends up.
According to a source close to the organization, the Sharks will be exploring several other roster moves, including ones via the trade market.