Height, who also played a key role in integrating the YWCA, died Tuesday of natural causes at Howard University Hospital in Washington, D.C., the council announced.
President Obama called Height "the godmother of the civil rights movement and a hero to so many Americans."
"Dr. Height devoted her life to those struggling for equality … and served as the only woman at the highest level of the civil rights movement — witnessing every march and milestone along the way," Obama said in a statement.
Beginning in the 1930s, Height helped shape the national agenda for the YWCA. Traveling throughout the nation, she advocated for interracial charters at a time when racial segregation was the norm and resistance to integration was often fierce.
As president of the National Council of Negro Women from 1957 to 1998, she led the group to expand its mission. Her initiatives included training thousands of women — housewives, teachers, office workers, students — to work as community advocates. Back in their own communities, they pushed for better housing, schools and stores. It was a way to help women escape what Height called the "triple bind of racism, sexism and poverty."
One of Height's most visible accomplishments was the Black Family Reunion Celebration, a three-day cultural event in Washington, D.C., with related events around the country. Founded to counter negative images of the black family, it has been held annually since 1986.
"Her fingerprints are quietly embedded in many of the transforming events of the last six decades as blacks, women and children pushed open and walked through previously closed doors of opportunity," Marian Wright Edelman, founder of the Children's Defense Fund, wrote in 2006 in the Baltimore Times.
Eleanor Smeal, president of the Feminist Majority Foundation, told The Times in an interview, "Dorothy understood from the beginning the importance of both the civil rights movement and the women's rights movement and how they're intertwined. She's always tried to keep people together and united."
The daughter of a nurse and a building contractor, Height was born March 24, 1912, in Richmond, Va., and grew up in Rankin, Pa., where she earned top grades in school.
After graduating from high school at 16, she was accepted to Barnard College in New York but was told she had to delay her entrance a year because the school had met its annual quota of two African American students.
Instead she entered New York University, which had no such quota. In four years she earned bachelor's and master's degrees in social work.
Height never married and had no children. She is survived by a sister, Anthenette Aldridge of New York City, and many nieces and nephews.
She joined the YWCA in 1937 and was there during a critical period in the organization's history as it grappled with the issue of race. In the 1940s, she pushed to end the YWCA's practice of separate conferences — one for black leaders and another for whites — and traveled the country helping local chapters implement the organization's interracial charter.
Heads of local chapters in the South would not meet with her, and she was forced to spend nights with local African American families because hotels would not admit black guests. A white police officer once threatened her life when she defied his order to wait for a train in the "colored waiting room," rather than on the platform with her white colleagues.
"He yelled again for me to go in the colored waiting room," she later wrote. "‘This is my train,' I called, starting to run, and he growled, ‘Don't you go straight on that train or I'll blow your brains out.'"
White colleagues surrounded her and together they got on the train. Later she reported the incident to Roy Wilkins, one of the leaders of the National Assn. for the Advancement of Colored People. "He said, ‘Dorothy, had you been a black man, you would have been dead.'"
Height was a 25-year-old assistant director at the YWCA in Harlem when then-First Lady Eleanor Roosevelt and National Council of Negro Women founder Mary McLeod Bethune paid a visit. Height was assigned the job of greeting and escorting the first lady, but a conversation with Bethune, the daughter of former slaves, altered the course of Height's life.