Initially working as a journalist for the Hull Advertiser he rose to be its Sub-editor and Manager. In 1861 he became a political correspondent working at the House of Commons for the Morning Star. In 1868 he resigned his position to become Assistant Editor to Alexander Russel in The Scotsman newspaper in Edinburgh. When Russel died in 1876 Cooper was placed to take over, but the position was partly filled by Robert Wallace for four years before Cooper eventually took over as full Editor in 1880. He served as editor for 25 years, until retiring in 1906 (aged 76) to be replaced by John Pettigrew Croal.
In 1890 he was elected a Fellow of the Royal Society of Edinburgh his proposers including Alexander Crum Brown, Sir Arthur Mitchell and John McLaren, Lord McLaren. The University of Edinburgh awarded him a Doctor of Letters (LLD) in 1907.
He is buried in Dean Cemetery in western Edinburgh with his wife Susanna who had died in 1887, and two of their sons: Frank Towers Cooper KC (1883-1915) and James Cooper (1866-1929). The grave lies on the north wall of the first north extension.
- Letters on Egypt (1891)
- Letters on South Africa (1895)
- An Editor’s Retrospect (1896) (an autobiography)
In 1852 he married Susannah Towers (d.1887). His second wife, Mabel, died in 1931.
- "1894 Charles A. Cooper". The Edinburgh Sir Walter Scott Club. Retrieved 17 June 2019.
- Scotsman: obituary 16 April 1916
- Edinburgh and Leith Post Office Directories 1888 onwards
- The Making of Modern Yorkshire, 1750-1914
- Dundee Courier: 17 April 1916