Prior to becoming a leading figure in the Christian countercult movement, Hanegraaff was closely affiliated with the ministry of D. James Kennedy of Coral Ridge Presbyterian Church in Florida. During his association with Kennedy in the 1980s, he applied memory-based techniques (such as acrostic mnemonics) to summarise strategies, methods and techniques in Christian evangelism. His work bears resemblances to memory dynamics techniques developed in speed-reading courses and in memory training programs used in some executive business courses.
During the late 1980s, Hanegraaff became associated with Walter Martin at the Christian Research Institute (CRI), the conservative Protestant countercult and apologetic ministry which Martin founded in 1960.
After Martin's death from heart failure in June 1989, Hanegraaff became president of CRI. As part of his role as ministry president, Hanegraaff assumed the role from Martin of anchorman on the radio program The Bible Answer Man. Hanegraaff became a conference speaker and itinerant preacher in churches, where he pursued the general ministry charter of CRI. Shortly after the release of Dan Brown's novel, he co-authored The DaVinci Code: Fact or Fiction? with Lutheran apologist Paul Maier. His most recent publication is Has God Spoken?, from Thomas Nelson in 2011.
The content of The Bible Answer Man show includes answering questions about Christian doctrine, biblical interpretation, and denominational particularities, as well as special focuses on particular issues when a notable figure is a guest, such as frequent shows focused on Mormonism when former Mormons appear in studio as guests to speak from their experiences.
Throughout the 1990s, Hanegraaff engaged in dialogue with Joseph Tkach, Jr. and other leaders of the Worldwide Church of God (WCG), now known as Grace Communion International (GCI). The WCG was founded in the 1930s by Herbert W. Armstrong, and had long been regarded as a cult by evangelicals, primarily for its denial of the Trinity and other traditional Christian doctrines. Following Armstrong's death in 1986, the group re-evaluated many of its teachings, including the British Israel doctrine and various eschatological predictions. Hanegraaff was one of a handful of evangelical apologists, including Ruth A. Tucker, who assisted in the reforms. The biggest changes to ensure their acceptance among evangelicals were in accepting the doctrine of the Trinity and salvation by grace through faith.
Hanegraaff sued longtime critic William Alnor for alleging that Hanegraaff's fundraising was under investigation for mail fraud. The allegation was based on an incident of misdirected mail which was followed by a January, 2005 CRI fundraising letter saying the error may have caused "perhaps hundreds of thousands of dollars" in donations to be lost. The defamation lawsuit was thrown out based on California's anti-SLAPP statute. The court found that although Alnor’s statements regarding a mail fraud investigation were false, Hanegraaff was unlikely to prove "actual malice.”
Answers in Genesis, a Christian ministry that insists on a literal, fundamentalist interpretation of the Bible starting from Genesis, accused Hanegraaff of unorthodox beliefs. One of the creation science movement's main spokesmen, Ken Ham, wrote in an article titled Hank Hanegraaff’s Abuse of Biblical Truth, "it [is] evident that Hanegraaff does not hold to a literal Genesis...as he was unwilling to understand Genesis in its most natural form—historical narrative...it actually gets worse: Hanegraaff also denies there was a literal serpent in the Garden of Eden that audibly spoke to Eve...Christians like Hanegraaff wholeheartedly accept many secular humanistic ideas like long-age geology and the big bang. When they accept these competing (anti-biblical) claims and mix them with their Christianity, something always has to give. Most people give up what the Bible plainly says..."
In his 1993 book Christianity in Crisis, Hanegraaff charged the Word of Faith movement with heretical teachings, saying that many of the Word of Faith groups were cults, and that those who knowingly accepted the movement's theology were "clearly embracing a different gospel, which is in reality no gospel at all."
Hanegraaff revisited some of the same issues in his 1997 book Counterfeit Revival, in which he rejected the claims of many charismatic teachers such as Rodney Howard Browne concerning what became known as the Toronto Blessing. The Toronto Blessing was associated with the Vineyard church located near the Toronto Airport, and was marked by spontaneous and sustained outbursts of bodily phenomena such as laughter, shaking, bouncing, and "resting in the Spirit." A different set of phenomena and claims subsequently emanated from churches in Brownsville, Pensacola, Florida, and became known as the Brownsville Revival.
One of the book's primary arguments is that many ostensible "manifestations of the Spirit" in charismatic, Pentecostal, and third wave affiliated churches are caused by psychological manipulation of parishioners, and that many of the "signs and wonders" claimed by these churches are fraudulent or result from manipulation, peer pressure, subtle suggestions, altered states of consciousness from repetitive chanting or singing, and expectations of supernatural events. Hanegraaff argues that many of the practices within these movements are not biblically sanctioned or appropriate, but have underlying aspects of scripture which are misinterpreted. He notes these movements rely too much on subjective experiences or feelings.
James A. Beverley, professor of theology and ethics at Tyndale Seminary (formerly Ontario Theological Seminary) in Toronto, Canada, reviewed Counterfeit Revival in Christianity Today, and wrote that while the book "exposes some real excesses and imbalances in the current charismatic renewal movements", it is a "misleading, simplistic, and harmful book, marred by faulty logic, outdated and limited research".
Hanegraaff responded on Equip.org by arguing that Beverley had received funding from Vineyard in the past and that he was aligned with them generally. Hanegraaff intimated that Beverley had been compensated to author the "hit piece" for Christianity Today.
In 2013, Hanegraaff published the book Afterlife: What You Need To Know About Heaven, The Hereafter & Near-Death Experiences where he addresses questions that were raised during his radio show regarding heaven and eternal life.
Hanegraaff was born in the Netherlands and raised in the United States since childhood. He and his wife Kathy have twelve children. They lived in Southern California but are now living in Charlotte, North Carolina. On Palm Sunday, 9 April 2017, Hanegraaff, together with his wife Kathy and two of his sons, were chrismated into the Eastern Orthodox Christian faith at St. Nektarios Greek Orthodox Church in Charlotte, NC (a parish that is part of the American Greek Archdiocese).
In 2017 Hanegraaff revealed that he has mantle cell lymphoma.