After dumping Thompson, Yahoo's board lured Mayer away from Google, where she had worked for 13 years. Yahoo's stock has climbed by about 60 percent since Mayer became CEO last July. The shares dipped 1 cent to $25.19 in Thursday's extended trading.
Amoroso, former CEO of TV listings provider Rovi Corp, said he is proud of Yahoo's progress since he became chairman.
"In that time, Yahoo hired a great new CEO, brought on a fantastic management team, revitalized the employee base, and has begun to release top-notch new products," he said in a statement. "With Marissa at the helm and the leadership team in place, this is a natural time for me to transition off the board."
Mayer praised Amoroso as a "wonderful" chairman. "Fred's mentorship and perspective has proved truly valuable to me in my first few months here at Yahoo," she said in a statement.