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At Bryn Mawr
In 1882, Thomas wrote a letter to the trustees of Bryn Mawr College, requesting that she be made president of the university. However, she was not granted the position as the trustee were concerned about her relative youth and lack of experience. Instead, Thomas entered in 1884 as the dean of the college and chair of English. Despite not receiving her desired role at Bryn Mawr, Thomas was active in the college's administration, working closely with then President James Rhoads. According to the biographical dictionary Notable American Women: 1607-1950, by 1892 she was "acting president in all but name".

At the end of April 1884 Thomas went with the encouragement of President Rhoads to tour other colleges in the area to become familiar with them in order to bring ideas back to Bryn Mawr. She started her tour at Vassar, then she went on to Smith College, Wellesley, Cambridge in Boston, and ended her tour at Radcliffe (or the Harvard Annex as it was still called at the time).

In 1885 Thomas, together with Mary Garrett, Mamie Gwinn, Elizabeth King, and Julia Rogers, founded The Bryn Mawr School in Baltimore Maryland. The school would produce well-educated young women who met the very high entrance standards of Bryn Mawr College.

In 1894, President Rhoads died, and Thomas was narrowly elected to succeed him on September 1, 1894. With respect to the President Rhoads's recent death, Thomas was not given any ceremony. She was president until 1922 and remained as Dean until 1908. During her tenure as president, Thomas' primary concern was upholding the highest standards of admissions and academic rigor. The entrance examinations for the college were made as difficult as those at Harvard University, and pupils could not gain admission by certificate. For the academic curriculum, Thomas emulated the "group system" of Johns Hopkins, in which students were required to take parallel courses in a logical sequence. Students could not freely choose electives. There were also other requirements, including a foreign language requirement that culminated in a sight translation examination proctored by Thomas herself. Overall, the academic curriculum at Bryn Mawr under Thomas shunned liberal arts education, preferring more traditional topics such as Greek, Latin, and mathematics. Thomas was also instrumental in bringing several new buildings to the College, which introduced collegiate Gothic architecture to the United States.

In 1908, she became the first president of the National College Women's Equal Suffrage League. She was also a leading member of the National American Woman Suffrage Association. After 1920 she advocated the policies of the National Woman's Party. She was one of the early promoters of an equal rights amendment to the U.S. Constitution.

Thomas lived for many years in a relationship with Mamie Gwinn. After Gwinn left Thomas in 1904 to marry (a love triangle fictionalized in Gertrude Stein's Fernhurst), Thomas started another relationship with Mary Garrett;[6] they shared the campus home, living together until Garrett's death. Miss Garrett, who had been prominent in suffrage work and a benefactor of Bryn Mawr, left to President Thomas $15,000,000 to be disposed of as she saw fit.[citation needed]. M. Carey Thomas had firm views on marriage, and in a letter to her mother she described it as a "Loss of freedom, poverty, and a personal subjection for which I see absolutely no compensation"