The son of Nationalist Party leader Eddie McAteer, Fergus was active in the civil rights movement of the late 1960s. He was arrested during the events of Bloody Sunday and charged with throwing stones, but the charges were later dropped. McAteer always strongly denied these claims.
McAteer himself became prominent in the Nationalist Party. In 1973, he was elected to Londonderry City Council, and he was re-elected in 1977. In October 1977 he merged the Nationalist Party with Unity to form the Irish Independence Party (IIP), becoming joint chair with former Unity leader Frank McManus. He stood for the party in Londonderry at the 1979 UK general election, but could take only fourth place in the poll. He held his seat on the City Council in 1981, with an increased vote. McAteer narrowly held the seat in 1985 and the IIP overall saw their representation on local councils reduced from 21 members in 1981 to 4 members in 1985 and dissolved before the next local election, and McAteer did not restand in 1989.
McAteer started an accountancy firm in 1973, and continues to run the firm.