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The 25-year-old was one of two players ordered to train with the Sparta women's team last year for saying "women belong at the stove" after a decision against him by a female assistant referee.
Koubek, who has won four caps for the Czech Republic, replaces Benoit Costil, who left Rennes for Bordeaux earlier in the close season.
"I'm very happy and proud to be chosen as the Rennes number one in their search for a new keeper," he said.
"In signing a long-term contract (four years), the club have shown me a lot of confidence. I will give my best."
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