Emma Helen Blair was born in Menasha, Wisconsin and went to high school in Massachusetts. In 1871, she returned to Wisconsin and attended Ripon College, from which she graduated in 1874. After teaching in public school for two years, she moved back to Wisconsin, and worked as a journalist in Milwaukee. In 1892, she began postgraduate studies in history, economics and sociology at Wisconsin State University. She became a librarian at the Wisconsin State Historical Society from 1894 to 1902, before resigning to become assistant to Reuben Gold Thwaites, translator of the 73-volume work Jesuit Relations (1896–1901). Emma participated in the editing and annotations of this massive work, and then assisted in the editing of the journals of the Lewis and Clark expeditions. In 1903, she began work on the project for which she is best remembered, the translation and editing of historical documents that were published in the 55-volume series The Philippine Islands, 1493-1898 (1903–09). Her collaborator on this project was James A. Robertson, later the librarian at the Philippines Library in Manila.
Her last work, published after her death, was the translation and editing of documents for The Indian Tribes of the Upper Mississippi Valley and Region of the Great Lakes (2 volumes, 1911–12).