The former Star Trek: The Next Generation cast member will play Dr Isaac Parrish on the series.
The character is the head of the Non-Lethal Weapons Lab at Global Dynamics.
Wheaton wrote about the news on his official blog today.
"I've had a great time developing his (Parrish's) backstory, creating his relationships with the characters, giving him secrets and beliefs, and doing all the other parts of character creation that make being an actor so much fun," he posted.
Wheaton's episode will air on July 23.
Eureka returns with new episodes on July 9 on Syfy.