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Jacobs was born at Gettysburg, Pennsylvania, the son of professor Michael and Juliana M (Eyster) Jacobs. He graduated from Pennsylvania College in 1862 and from the Lutheran Theological Seminary at Gettysburg in 1865. Between 1870 and 1883, he was professor at Pennsylvania College. He was then appointed professor of systematic theology in The Lutheran Theological Seminary in Mount Airy, where he also assumed the office of dean in 1894. In 1920, he became President of the Seminary when the office of dean was abolished.

He served as president of his church's board of foreign missions (1902–07), of the General Conference of Lutherans (1899, 1902, 1904), of the American Society of Church History (1907–08), and of the Pennsylvania German Society (1910–11). He also translated various German theological works and editing the Lutheran Church Review (1882-96), and Lutheran Commentary (1895-98). Henry Eyster Jacobs, working with John A.W. Haas, published The Lutheran Cyclopedia in 1899.

Lutheran Archives Center in Philadelph holds a large collections of materials relating to Lutheran clergy, theologians and church workers including personal papers of Henry Eyster Jacobs.