Zuccarelli was named to the board by Governor Pat Quinn.
That drew fire from Bill Daley, a democratic challenger in the race for governor.
He called the appointment political cronyism and said Zuccarelli was a double-dipper because he already holds his supervisor post in Thornton Township.
In a statement issued Tuesday afternoon, Gov. Quinn said: "I felt he would have brought an important perspective to the CTA Board, which has all too often left this region behind when it came to important transportation access issues. I accept Frank's decision and will soon announce his replacement."