In 1990, Mooney was elected a vice president of the AFT. He served on the AFT's executive council, the governing body of the national union, and in 1998 became part of the council's executive committee—a body of executive council members close to the president of the AFT, which advises the president and debates and formulates policy before bringing it to the council. On the executive council, Mooney served on the human rights and community relations, organizing, and affiliate accountability committees. He was also chair of the "program and policy council" for the union's teacher division.