Boyd was raised Roman Catholic, but became an atheist as a teen. In 1974, at the age of 17, he committed his life to Christ. He graduated cum laude from Yale Divinity School (1982) and magna cum laude from Princeton Theological Seminary (1987). He was Professor of Theology at Bethel University for 16 years, where he continues to teach on an adjunct basis. His Princeton dissertation (published as Trinity and Process) was a critique of the process theology of Charles Hartshorne. Here, Boyd attempts to construct a philosophical theology that retains the positive features of a process worldview, while avoiding its unorthodox implications. Boyd is widely known for his award-winning book Letters From a Skeptic (1994). This book is a collection of letters written by Boyd and his father Edward, who was an atheist at the time. Through the course of their correspondence, Boyd addressed many of the perennial intellectual challenges to the Christian faith, which led to his father's conversion.

Boyd is also a former Oneness Pentecostal, and wrote the book Oneness Pentecostals and the Trinity (1992), critiquing the movement's anti-trinitarian view of God and other doctrines. Boyd is also known as an exponent of open theism, which he explores in the book God of the Possible (2000). In essence, open theism is the view that the future is partly open, and therefore known to God partly as a realm of possibilities. Proponents of the conservative or traditional view of God within the Baptist General Conference tried unsuccessfully to have the rules of the denomination changed to exclude Boyd and other open theists.

Boyd was featured in a front-page New York Times profile in July 2006, after losing 20% of his congregation because he refused to lend his public support to conservative political causes, and directly challenged the highly politicized nature of much American evangelical Christianity. In his view, the "Kingdom of God" always looks like Jesus Christ, and therefore cannot be associated with any particular political or nationalistic ideology. The congregational loss, as well as his view, stem from a 2004 sermon series that he spoke called "The Cross and the Sword." In the same vein, he authored the book The Myth of a Christian Nation: How the Quest for Political Power Is Destroying the Church (2006), in which he argues that a commitment to non-violence and to loving one's enemies lies at the heart of the teachings of Jesus. Boyd expressed these views when he was featured in the CNN documentary God's Warriors, hosted by Christiane Amanpour, which aired in August 2007. In a more recent book, The Myth of a Christian Religion: Losing Your Religion for the Beauty of a Revolution (2009), he presents his understanding of what the Kingdom of Jesus is.

Boyd is well-known for his academic work on the topics of Satan and the demonic, the problem of evil, and "spiritual warfare." He is authoring a series of books, titled "Satan and Evil" (produced by InterVarsity Press), two volumes of which have already been published: God at War: The Bible and Spiritual Conflict (1997) and Satan and the Problem of Evil: Constructing a Trinitarian Warfare Theodicy (2001). In between numerous other projects, he has been at work on the next installment of this series, tentatively titled The Myth of the Blueprint, which is now planned as a two-volume work with roughly 1,000 pages to each volume. Related to this, Boyd is a leading exponent of the "Christus Victor" model of the atonement.

Boyd is also a notable figure in New Testament scholarship and the Quest for the Historical Jesus. He is critical of liberal scholarship as typified by the Jesus Seminar as well as the individual work of scholars like John Dominic Crossan and Burton Mack. In 2010, Boyd was listed as one of the twenty most influential Christian scholars alive today. He participates in numerous public debates, most notably with friend and religious skeptic Robert M. Price (who questions the very existence of a historical Jesus) on the historicity of the New Testament and related matters. His first book in this area was Cynic Sage or Son of God? (1995). More recently, his book (co-authored with Paul Rhodes Eddy), The Jesus Legend: A Case for the Historical Reliability of the Synoptic Jesus Tradition (2007) won the 2008 Christianity Today Book of the Year Award (Biblical Studies category).