Anna "Annie" Julia Cooper was born into enslavement in Raleigh, North Carolina, in 1858 to Hannah Stanley Haywood, an enslaved woman in the home of prominent Wake County landowner George Washington Haywood. Either George or his brother Fabius J. Haywood are thought to be Cooper's Father. Cooper worked as a domestic servant in the Haywood home and had two older brothers, Andrew J. Haywood and Rufus Haywood. Andrew was a slave of Dr. Fabius J. Haywood, and he later served in the Spanish–American War. Rufus was also born a slave and was the leader of the music group Stanley's Band.

In 1868, when Cooper was nine years old, she received a scholarship and began her education at the newly opened Saint Augustine's Normal School and Collegiate Institute in Raleigh, founded by the local Episcopal diocese for the purpose of training teachers to educate former slaves and their families. The Reverend J. Brinton offered Cooper a scholarship to help pay for her expenses. According to Mark S. Giles, a Cooper biographer, "the educational levels offered at St. Augustine ranged from primary to high school, including trade-skill training." During her 14 years at St. Augustine's, she distinguished herself as a bright and ambitious student who showed equal promise in both liberal arts and analytical disciplines such as math and science; her subjects included languages (Latin, French, Greek), English literature, math, and science. Although the school had a special track reserved for women – dubbed the "Ladies' Course" – and the administration actively discouraged women from pursuing higher-level courses, Cooper fought for her right to take a course reserved for men, by demonstrating her scholastic ability. During this period, St. Augustine's pedagogical emphasis was on training young men for the ministry and preparing them for additional training at four-year universities. One of these men, George A. C. Cooper, would later become her husband. He died after only two years of marriage.

Cooper's academic excellence enabled her to work as a tutor for younger children, which also helped her pay for her educational expenses. After completing her studies, she remained at the institution as an instructor. In the 1883–84 school year she taught classics, modern history, higher English, and vocal and instrumental music; she is not listed as faculty in the 1884–85 year, but in the 1885–86 year she is listed as "Instructor in Classic, Rhetoric, Etc." Her husband's early death may have contributed to her ability to continue teaching; had she stayed married, she might have been encouraged or required to withdraw from the university to become a housewife.

After her husband's death, Cooper entered Oberlin College in Ohio, where she continued to follow the course of study designated for men. Her classmates were Ida Gibbs (later Hunt) and Mary Church Terrell. After teaching briefly at Wilberforce College, Cooper returned to St. Augustine's in 1885. She then went back to Oberlin and earned an M.A. in Mathematics in 1887.

During her years as a Teacher and principal at M Street High School in Washington, D.C., Cooper completed her first book, A Voice from the South: By a Black Woman of the South, published in 1892, and also delivered many speeches calling for civil rights and women's rights. Perhaps her most well-known volume of writing, A Voice from the South is widely viewed as one of the first articulations of Black feminism. The book advanced a vision of self-determination through education and social uplift for African-American women. Its central thesis was that the educational, moral, and spiritual progress of black women would improve the general standing of the entire African-American community. She says that the violent natures of men often run counter to the goals of higher education, so it is important to foster more female intellectuals because they will bring more elegance to education. This view was criticized by some as submissive to the 19th-century cult of true womanhood, but others label it as one of the most important arguments for black feminism in the 19th century. Cooper advanced the view that it was the duty of educated and successful black women to support their underprivileged peers in achieving their goals. The essays in A Voice from the South also touched on a variety of topics, such as race and racism, gender, the socioeconomic realities of black families, and the administration of the Episcopal Church.

Cooper was an author, educator, and public speaker. In 1893, she delivered a paper entitled "The Intellectual Progress of the Colored Women of the United States since the Emancipation Proclamation" at the World's Congress of Representative Women in Chicago. Cooper was one of five African American women invited to speak at this event, along with: Fannie Barrier Williams, Sarah Jane Woodson Early, Hallie Quinn Brown, and Fanny Jackson Coppin.

She was also present at the first Pan-African Conference in London in 1900 and delivered a paper entitled "The Negro Problem in America."

In 1914, at the age of 56, Cooper began courses for her doctoral degree at Columbia University, but was forced to interrupt her studies in 1915 when she adopted her late half-brother's five children upon their mother's death. Later on she transferred her credits to the University of Paris-Sorbonne, which did not accept her Columbia thesis, an edition of Le Pèlerinage de Charlemagne. Over a decade she researched and composed her dissertation, completing her coursework in 1924. Cooper defended her thesis The Attitude of France on the Question of Slavery Between 1789 and 1848 in 1925. At 65, she became the fourth black woman in American history to earn a Doctorate of Philosophy degree.

Although the alumni magazine of her undergraduate alma mater, Oberlin College, praised her in 1924, saying, "The class of ’84 is honored in the achievement of this scholarly and colored alumna," when she tried to present her edition of Le Pèlerinage de Charlemagne to the college the next year, it was rejected.

Cooper's other writings include her autobiographical booklet The Third Step, about earning her doctorate from the Sorbonne, and a memoir about the Grimké family, entitled "The Early Years in Washington: Reminiscences of Life with the Grimkés," which appeared in Personal Recollections of the Grimké Family and the Life and Writings of Charlotte Forten Grimké (privately published in 1951).

On February 27, 1964, Cooper died in Washington, D.C., at the age of 105. Her memorial was held in a chapel on the campus of Saint Augustine's College, in Raleigh, NC where her academic career began. She was buried alongside her husband at the City Cemetery in Raleigh.

Also in 2009, a tuition-free private middle school was opened and named in her honor, the Anna Julia Cooper Episcopal School on historic Church Hill in Richmond, Virginia.

She later moved to Washington, DC – where she would develop a close friendship with Charlotte Forten Grimké – Cooper began teaching at M Street High School, becoming principal in 1901.

Pages 24 and 25 of the 2016 United States passport contain the following quotation: "The cause of freedom is not the cause of a race or a sect, a party or a class – it is the cause of humankind, the very birthright of humanity." – Anna Julia Cooper