Cotter was born into the Norse-Gaelic Cotter family, the son of James Cotter the Younger (1689–1720), a leading Roman Catholic and Jacobite in County Cork, by his marriage to Margaret Mathew.

[1] After his father's death, he was brought up by guardians as a Protestant and educated at Midleton College, a Church of Ireland boarding school in County Cork [2][3] and Trinity College Dublin.

Cotter served as a Member of Parliament for Askeaton in the Irish House of Commons between 1761 and 1768.

[1] On 11 August 1763 he was created a baronet, of Rockforest in the County of Cork, in the Baronetage of Ireland.

[4][5] In 1746 Cotter married Arabella Rogerson, daughter of Sir John Rogerson, Lord Chief Justice of Ireland, and Elizabeth Ludlow.