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 help develop and spread strategies and methods for personal Christian evangelism.

As part of his duties, Hanegraaff took over from Martin the role of anchorman on the radio program The Bible Answer Man and became a conference speaker and itinerant preacher in churches, where he pursued the general ministry charter of CRI.

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 allegation was based on an incident of misdirected mail, which was followed by a January 2005 CRI fundraising letter saying the error might have caused "perhaps hundreds of thousands of dollars" in donations to be lost.

"[6] 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.

One of the book's primary arguments is that many ostensible "manifestations of the Spirit" in Pentecostal, Charismatic, and Neo-Charismatic or "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, or expectations of supernatural events.

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current charismatic renewal movements", it is a "misleading, simplistic, and harmful book, marred by faulty logic [and] outdated and limited research".