Das Verhältniss des Jakobus, Bruders des Herrn, zu Jakobus Alphäi (1842, 1843)
The Principle of Protestantism as Related to the Present State of the Church (1845)
What is Church History? A Vindication of the Idea of Historical Development (1846)
The Birth Day of the Church (1850)
Neander’s Life of Christ (1848)
The Life and Character of St. John (1850)
Recollections of Neander (1851)
History of the Apostolic Church: With a General Introduction to Church History (1851, 1853)
Neander as a Church Historian (1852)
German Theology and the Church Question (1852, 1853)
The Life and Labours of St. Augustine: A Historical Sketch (1854)
The Evangelical Church Diet of Germany (1857)
The State Church System in Europe (1857)
The Evangelical Alliance at Berlin (1857)
Christianity in America (1857)
Germany: Its Universities, Theology, and Religion (1857)
The Influence of the Early Church on the Institution of Slavery (1858)
The Conflict of Trinitarianism and Unitarianism in the Ante-Nicene Age (1858)
The Oldest Opposition to Christianity, and Its Defense (1858)
History of the Christian Church, Vol. 1 (1858, 1910)
The Crystal Palace at Sydenham (1859)
Slavery and the Bible: A Tract For the Times (1861)
The Heidelberg Catechism (1863)
The Tercentenary Jubilee of the Heidelberg Catechism (1863)
The Anglo-American Sabbath (1863)
Constantine the Great, and the Downfall of Paganism in the Roman Empire (1863)
The Saints of the Desert: St. Anthony of Egypt, and Symeon the Stylite (1864)
The Donatist Controversy (1864)
Lange's Theological and Homiletical Commentary (1864)
Leo the Great and the Papacy in the Fifth and Sixth Centuries (1864)
The Hagiology and Hagiolatry of Romanism (1865)
The Development of the Ancient Catholic Hierarchy (1865-1866)
The Person of Christ: The Miracle of History (1865)
The Person of Christ: The Perfection of His Humanity Viewed as a Proof of His Divinity (1865, 1880)
The Patristic Doctrine on the Eucharist (1866)
The Ecumenical Councils (1866)
The Monophysite Churches of the East (1866)
Greek and Latin Hymnology (1866)
The Genius and Theology of St. Augustine (1867)
History of the Christian Church, Vol. 2 (1867, 1870)
History of the Christian Church, Vol. 3 (1867)
Christ in Song: Hymns of Immanuel (1868)
The Romance of M. Renan, and the Christ of the Gospels (1868)
Letter Book, Vol. 1 (1868-1869)
Letter Book, Vol. 2 (1869-1870)
Letter Book, Vol. 3 (1870-1871)
Letter Book, Vol. 4 (1871-1874)
The Theology For Our Age and Country (1872)
The Old Catholic Church (1873)
Hymns and Songs of Praise For Public and Social Worship (1874)
A Commentary on the Holy Scriptures, Vol. 8: The Book of Job (1874)
Letter Book, Vol. 5 (1874-1876)
Calvin’s Life and Labors (1875)
The Vatican Decrees in Their Bearing on Civil Allegiance: A Political Expostulation (1875)
Letter Book, Vol. 6 (1876-1878)
The Heidelberg Catechism (1876)
In Memoriam: Our Children in Heaven (1876)
The Harmony of the Reformed Confessions (1877)
The Creeds of Christendom, Vol. 1 (1877)
The Creeds of Christendom, Vol. 2 (1877, 1896)
The Creeds of Christendom, Vol. 3 (1877)
Through Bible Lands: Notes of Travel in Egypt, the Desert, and Palestine (1878)
Letter Book, Vol. 7 (1878-1880)
Disputed Scripture Localities (1878)
The Anglo-American Bible Revision (1879)
Progress of Christianity in the United States of America (1879)
Anglo-American Bible Revision (1879)
The Resurrection of Christ: The Test of Christianity (1880)
The Chronology of the Life of Christ (1880)
The Peter of History and the Peter of Fiction (1880)
A Christian Catechism for Sunday-Schools and Families (1880)
A Dictionary of the Bible (1880, 1887)
Letter Book, Vol. 8 (1880-1881)
The Old Version and the New (1881)
The Revised New Testament (1881)
Review of Victor Ryssel, Gregorius Thaumaturgus (1881)
The Epistle of Paul to the Galatians (1881)
A Library of Religious Poetry: A Collection of the Best Poems of All Ages and Tongues (1881)
Introduction to Westcott & Hort, The New Testament in the Original Greek (1881)
Rationalistic Testimonies to Christ (1882)
The Gospel According to Matthew (1882)
The Revised Version and Its Critics (1883)
A Companion to the Greek Testament and the English Version (1883, 1903)
The Probable Fate of the Revision (1883)
Montanism and Its Modern Representatives (1883)
The Oldest Church Manual Called the Teaching of the Twelve Apostles: The Didache (1885)
Documentary History of the American Committee on Revision (1885)
Christ and Christianity (1885)
The Idiom and Vocabulary of the Teaching of the Twelve Apostles (1885)
Saint Augustin, Melanchthon, Neander: Three Biographies (1886)
History of the Christian Church, Vol. 4 (1886, 1905)
The Confessions of Augustine (1886)
John Chrysostom, the Greatest Preacher of the Greek Church: A Sketch of His and Work (1888)
Chrysostom at Constantinople (1888)
History of the Christian Church, Vol. 6 (1888, 1904)
The Progress of Religious Freedom as Shown in the History of Toleration Acts (1889)
The Revision of the Westminster Confession of Faith (1889)
Creed Revision in the Presbyterian Churches (1890)
Dante and the Divina Commedia (1890)
Did Luther Commit Suicide? (1890)
Laurentius Valla: A Pioneer of Historical Criticism (1891)
Heinrich Bullinger, the Successor of Zwingli and Second Antistes of Zurich (1891)
The Renaissance and the Reformation (1891)
The Renaissance: The Revival of Learning and Art in the Fourteenth and Fifteenth Centuries (1891)
Saint Chrysostom and Saint Augustin (1891)
Introduction to Emanuel V. Gerhart, Institutes of the Christian Religion (1891)
The Friendship of Calvin and Melanchthon (1892)
Other Heresy Trials and the Briggs Case (1892)
Calvin as a Commentator (1892)
A Tribute to John Calvin (1892)
History of the Christian Church, Vol. 7 (1892)
The Semi-Centennial of Philip Schaff: Berlin 1842 - New York 1892 (1893)
Institutions of Learning in the Middles Ages (1893)
Scholastic and Mystic Theology in the Middle Ages (1893)
Presbyterian Theology in America: The Old School Theology (1893)
The Reunion of Christendom (1893)
The American Church History Series, Vol. 1: The Religious Forces of the United States (1893)
Passion Week in Rome Fifty Years Ago (1895)
The American Church History Series, Vol. 13: A History of American Christianity (1897)
The Life of Philip Schaff: In Part Autobiographical (1897)
The Life of Dr. Philip Schaff (1899)
The American Church History Series, Vol. 5: A History of the Methodists in the United States (1899)
History of the Christian Church, Vol. 5, Pt. 1 (1907)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 1 (1908)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 2 (1908)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 3 (1909)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 4 (1909)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 5 (1909)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 6 (1910)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 7 (1910)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 8 (1910)
History of the Christian Church, Vol. 5, Pt. 2 (1910, 1930)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 9 (1911)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 10 (1911)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 11 (1911)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 12 (1912)
The New Schaff-Herzog Encyclopedia of Religious Knowledge, Vol. 13 (Index) (1914)