Katharine Jefferts Schori, bishop of the Episcopal diocese of Nevada, was elected at the US Anglican church's general convention in Columbus, Ohio, after five ballots.
Seven candidates stood for the post of the church's 26th presiding bishop.
"The decision today is the fruit of the witness and ministry of women bishops, priests, and deacons in the life of our church," current Presiding Bishop and Primate Frank Griswold said in a statement on the church's website.
"Bishop Jefferts Schori is a person gifted in mind, heart and spirit, and I am fully confident that the Church and the Communion will be blessed by her ministry in the years ahead," Mr Griswold said.
Mrs Schori, 52, has a doctorate in oceanography and has worked with the US National Marine Fisheries Service.
She is married to a professor of topology and has one daughter who is an officer in the US Air Force, according to a biography.
Mrs Schori's win signals a victory for women in the 2.3 million-member Episcopal Church, the US branch of the Anglican Union.
Most of the branches of the Anglican Union around the world have resisted elevating women to bishops.
In recent years the US church has also been torn over the issue of electing homosexual bishops.
In 2003 the church endorsed the election of its first openly gay bishop, Gene Robinson, in the eastern diocese of New Hampshire, but the move did not put an end to the divide over the issue.
The church narrowly avoided widening the schism in early May when it chose a heterosexual to head its California diocese over three rival openly gay candidates.