She was born into an Anglican family, at Astley in Worcestershire. Her father, William Henry Havergal (1793—1870), was a clergyman, writer, composer, and hymnwriter. Her brother, Henry East Havergal, was a priest in the Church of England and an organist.

In 1852/3 she studied in the Louisenschule, Düsseldorf, and at Oberkassel. Otherwise she led a quiet life, not enjoying consistent good health; she travelled, in particular to Switzerland. She supported the Church Missionary Society.

She died of peritonitis at Caswell Bay on the Gower Peninsula in Wales. Her sisters saw much of her work published posthumously. Havergal College, a private girls' school in Toronto, is named after her. The composer Havergal Brian adopted the name as a tribute to the Havergal family.