The Royals announced on Tuesday that Pena cleared outright waivers and has been assigned to their Triple-A Omaha club.
Pena was designated for assignment on April 24 when Jose Guillen came off the disabled list. The Royals liked Pena and were apprehensive that, in a catcher-thin market, he might be claimed off waivers, but he was not.
"That's unfortunate for Brayan personally, but I'm glad we've still got him," manager Trey Hillman said. "There are a lot of things about Brayan I like -- his energy, the improvement I saw defensively in Spring Training, and he got in two big ballgames for us and did well."
Pena spent the first 2 1/2 weeks of the season as the Royals' third-string catcher and pinch-hitter, going 2-for-7 with two doubles and one RBI.
Dick Kaegel is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.