Height, who continued actively speaking out into her 90s, had been at Howard University Hospital for some time. The hospital said in a statement she died of natural causes.
As a teenager, Height marched in New York's Times Square shouting, "Stop the lynching." In the 1950s and 1960s, she was the leading woman helping the Rev. Martin Luther King Jr. and other activists orchestrate the civil rights movement.
Obama spoke of the environment in which Height was raised, where lynching was still commonplace and many black people were denied opportunity.
Some of the women at the cathedral wore bright hats like Height used to wear.
Leaders from Congress shared the front row with the president. Several officials from Obama's cabinet also were in attendance. Republican National Committee chairman Michael Steele also was expected to attend.
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