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After her father died she moved to Cambridge, but soon after returned to London. Touched by the poverty in the eastend of London in 1868 she opened the Home of Industry at 60 Commercial Road in Spitalfield.
In the 1870s, she organised that Home children were sent to Canada from her home in London also had arrangements with Barnardo's Homes of Dr. Barnardo in London, Quarriers homes in Scotland, and Smyly homes in Dublin, Ireland similar to arrangements with English and Scottish homes. In Canada she had set up a number of Homes, Marchmont, Galt in Ontario and in Knowlton Quebec 
The Doyle Report of 1875 into the emigration of children from these homes cast a shadow over the process of exporting children although it acknowledged the benevolent motives of MacPherson and others.
Her sister Louisa MacPherson married Charles Henry Birt, and helped her sister in her mission. In 1873 she established a home in Liverpool called The Sheltering Home.
- Annie Mac Pherson British Home Children.
- Annie MacPherson
- Young Immigrants to Canada Smyly Homes of Dublin, Ireland.
- The golden bridge: young immigrants to Canada, 1833-1939 By Marjorie Kohli
- Gods answers, a record of Miss Annie Macphersons work at the Home of Industry, Spitalfields, London, and in Canada by Clara M.S. Lowe, (Introduction by )Rev. John Macpherson, LONDON: JAMES NISBET & CO (1882)
- Doyle Report into MacPherson and Rye
- Louisa Birt
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