- Among the Forces
- Collected Essays, Volume V: Science and Christian Tradition: Essays
- Creation and Its Records: A Brief Statement of Christian Belief with Reference to Modern Facts and Ancient Scripture
- Evolution: An Investigation and a Critique
- Fables of Infidelity and Facts of Faith: Being an Examination of the Evidences of Infidelity
- Lectures and Essays
- Life: Its True Genesis
- Monism as Connecting Religion and Science: A Man of Science
- Natural Law in the Spiritual World
- Science and Morals and Other Essays
- Science and the Infinite; or, Through a Window in the Blank Wall
- The Necessity of Atheism
- The Relations Between Religion and Science: Eight Lectures Preached Before the University of Oxford in the Year 1884
- The Story of Creation as Told By Theology and By Science
- The Theories of Darwin and Their Relation to Philosophy, Religion, and Morality
- Thoughts on Religion