In 1991 he started working in the field of Dawah, and founded the Islamic Research Foundation (IRF). Naik’s wife, Farhat Naik, is the President of the women’s section of the Islamic Research Foundation (IRF).

His first debate was in 1994, a debate on the views of writer Taslima Nasreen on Islam in her book Lajja, organised at the “Mumbai Marathi Patrakar Sangh”, entitled “Is Religious Fundamentalism a Stumbling block to Freedom of Expression?”. With the presence of four journalists, the debate went on for hours. In April 2000, Naik debated with William Campbell in Chicago on the topic of “The Qur’an and the Bible: In the Light of Science”, one of his most-cited debates. On 21 January 2006 Naik held an inter-religious dialogue with Ravi Shankar in Bangalore about the concept of God in Islam and Hinduism. In February 2011 Naik addressed the Oxford Union via video link from India. Every year since November 2007 Naik has led a 10-day Peace Conference at Somaiya Ground, Sion, Mumbai. Lectures on Islam have been presented by Naik and twenty other Islamic speakers.

In 2004 Naik, at the invitation of the Islamic Information and Services Network of Australasia, made an appearance at the University of Melbourne, where he argued that only Islam gave women true equality. He said the more “revealing Western dress” makes women more susceptible to rape. Sushi Das of The Age commented that “Naik extolled the moral and spiritual superiority of Islam and lampooned other faiths and the West in general”, further stating that Naik’s words “fostered a spirit of separateness and reinforced prejudice”.

Naik said in 2006 that he was inspired by Ahmed Deedat, an Islamic preacher whom he met in 1987. (Naik is sometimes referred to as “Deedat plus”, a label given to him by Deedat.)

In August 2006, Naik’s visit and conference in Cardiff caused controversy when Welsh MP David Davies called for his appearance to be cancelled. He said Naik was a “hate-monger”, and that his views did not deserve a public platform. Muslims from Cardiff, however, defended Naik’s right to speak in the city. Saleem Kidwai, Secretary General of the Muslim Council of Wales, stated that “people who know about him [Naik] know that he is one of the most uncontroversial persons you could find. He talks about the similarities between religions, and how should we work on the common ground between them”, whilst also inviting Davies to discuss further with Naik personally in the conference. The conference went ahead, after the Cardiff council stated it was satisfied that he would not be preaching extremist views.

In The Wall Street Journal, Sadanand Dhume criticised Naik for recommending the death penalty for homosexuals and for apostasy from the faith. He also criticised him for calling for India to be ruled by Shariah law. He added that, according to Naik, Jews “control America” and are the “strongest in enmity to Muslims.” He maintained that Naik supports a ban on the construction of non-Muslim places of worship in Muslim lands as well as the Taliban’s bombing of the Buddhas of Bamiyan. Dhume argues that people reportedly drawn to Naik’s message include Najibullah Zazi, the Afghan-American arrested for planning suicide attacks on the New York subway; Rahil Sheikh, accused of involvement in a series of train bombings in Mumbai in 2006; and Kafeel Ahmed, the Bangalore man fatally injured in a failed suicide attack on Glasgow airport in 2007. He also stated that “unless Indians find the ability to criticise such a radical Islamic preacher as robustly as they would a Hindu equivalent, the ideal of Indian secularism would remain deeply flawed.”

In 2007, reports claimed that Darul Uloom considered him a self-styled preacher unattached to any of the four orthodox Sunni Islamic schools of jurisprudence (fiqh) and therefore has issued many fatwas against Zakir Naik, rejecting him as being amongst the ghair muqallidin (a term used in Islam to describe someone who does not relate with the four madhabs viz. Hanafi, Hanbali, Sha’afi and Maliki) thereby appealing towards Muslims to avoid listening to his sermons. In 2016, a Darul Uloom spokesman clarified reports that although a few fatwas had been issued by Darul Uloom against Naik on legal matters, these were being “deliberately highlighted” by the media. The deputy vice chancellor of Darul Uloom, Abdul Khaliq Madrasi, came out in his support, saying: “We have bad differences of opinion with Zakir Naik. But he is recognized as an Islamic scholar the world over. We don’t believe that he could be connected with terrorism in any way.”

In a lecture delivered on 31 July 2008 on Peace TV, Naik commented on the attacks of 11 September: “it is a blatant, open secret that this attack on the Twin Towers was done by George Bush himself”. He also said that “even a fool will know” that the 9/11 attacks were “an inside job” orchestrated by US President George W. Bush.

In 2008, an Islamic scholar in Lucknow, shahar qazi Mufti Abul Irfan Mian Firangi Mahali, issued a fatwa against Naik, claiming that he supported Osama bin Laden, and that his teachings were un-Islamic. Naik claims his speeches were being taken out of context.

Najibullah Zazi, the Afghan-American linked to Al-Qaeda who was found guilty in the 2009 New York City Subway and United Kingdom plot was an “admirer” of Naik’s sermons. When Time hinted that his preachings could have inspired Najibullah Zazi’s terrorist activities, Naik insisted: “I have always condemned terrorism, because according to the glorious Koran, if you kill one innocent person, then you have killed the whole of humanity.”

Naik was ranked 89 on The Indian Express’s list of the “100 Most Powerful Indians in 2010”. He was ranked 82 in the 2009 edition. According to Praveen Swami, Naik is “perhaps the most influential Salafi ideologue in India”. Sanjiv Buttoo says he is acknowledged as an authority on Islam, but is known for making negative remarks about other religions. Sadanand Dhume writes that Naik has a “carefully crafted image of moderation”, because of his gentle demeanour, his wearing of a suit and tie, and his quoting of scriptures of other religions. He is also listed in the book The 500 Most Influential Muslims under honourable mention, in the 2009, 2010, 2011, 2012, 2013/2014, 2015/2016, 2017, 2018, 2019 editions.

Naik was denied entry into the United Kingdom and Canada in June 2010. Naik was forbidden to enter Canada after Tarek Fatah, founder of the Muslim Canadian Congress, warned MPs of Naik’s views. He was banned from entering the UK by the then Home Secretary Theresa May after arranging to give talks in London and Sheffield. May said of the exclusion order, “Numerous comments made by Dr Naik are evidence to me of his unacceptable behaviour”. Naik argued that the Home Secretary was making a political decision, not a legal one, and his lawyer said the decision was “barbaric and inhuman”. He also claimed that his comments were taken out of context. Film producer Mahesh Bhatt supported Naik, saying the ban constituted an attack on freedom of speech. It was reported that Naik would attempt to challenge the ruling in the High Court. His application for judicial review was dismissed on 5 November 2010.

Dismissing Darwin’s Theory of Evolution, Naik said that the theory of evolution is “only a hypothesis, and an unproven conjecture at best”. According to Naik, most scientists “support the theory, because it went against the Bible – not because it was true.” Naik argues that scientific theories were prophesied by the Quran. For example, he has stated in 2010 that certain verses of the Quran accurately describe embryological development.

Later in 2010, Naik said that he had been quoted out of context regarding the remarks on terrorism. “As far as terrorist is concerned”, he said, “I tell the Muslims that every Muslim should be a terrorist… What is the meaning of the word terrorist? Terrorist by definition means a person who terrorises. So in this context every Muslim should be a terrorist to each and every anti-social element. I’m aware that terrorist is more commonly used for a person who terrorises innocent human beings. So in this context no Muslim should ever terrorise a single innocent human being.”

The Islamic Research Foundation website describes Naik as “the ideologue and driving force behind Peace TV Network”. Naik’s channel is to promote “Truth, Justice, Morality, Harmony and Wisdom for the whole of humankind”, mentions its website. The Indian government banned the Peace TV channel in 2012. According to The New York Times in 2015, quoting an anonymous Indian journalist, the Mumbai police have barred him from holding conferences “because he stirs controversy”, and Indian satellite providers have refused to broadcast his television channel, Peace TV. However, as of August 2019, Peace TV was still available in India through a free app in the Google Play Store, which had been downloaded over a lakh (100,000) times.

In 2014, Naik visited Gambia at the invitation of President Yahya Jammeh to attend the grand celebration of Gambian revolution’s 20th anniversary. There he delivered four lectures between 11 and 22 October. The lectures took place in University of the Gambia, Pancha Mi Hall of Paradise Suites Hotel, presidents home village Kanilai, Foni Kansala and Kairaba Beach Hotel, Kololi. Gambian cabinet ministers, religious leaders, students and thousands of people attended his lectures on subjects including “Terrorism and Jihad: an Islamic perspective”, “religion in the right perspective”, “Dawah or destruction?” and “the misconceptions about Islam”. Meanwhile, he also met with the president Yahya Jammeh along with Gambia Supreme Islamic Council and held an Islamic conference with the Imams of Gambia.

In 2016, during a press conference Naik claimed himself to be a non-resident Indian (NRI). In 2017, according to the Middle East Monitor, Naik was granted citizenship by Saudi Arabia.

Naik delivered another six lectures in April 2016. Two of his lectures in Malaysia, entitled “Similarities between Hinduism and Islam” and “Is the Quran God’s word?” were objected by HINDRAF, along with other NGOs, saying that these lectures might provoke inter-racial tensions. With the initial support of the Government authority, the event went ahead as planned.

After revealing the investigations of the Dhaka Terror Attack in July 2016 published by The Daily Star that a terrorist involved in the brutal killings followed Zakir Naik’s page on Facebook and was influenced by Naik’s speeches, The terrorist had posted sermons of Zakir Naik on social media where Naik urged “all Muslims to be terrorists” Indian Union Minister of State for Home Affairs Kiren Rijiju said, “Zakir Naik’s speech is a matter of concern for us. Our agencies are working on this.” He was then termed a controversial as well as a popular figure by the media. After 2 days in investigation, the Maharashtra State Intelligence Department (SID) gave a clean chit to Zakir Naik and said that Naik would not and cannot be arrested on his return to India as the probe ordered by the Maharashtra government did not find any other strong evidence to link Naik to terror-related activities. The Daily Star apologized to Naik over the Dhaka Terror Attack controversy and stated that they never blamed him for the attack. The newspaper quoted that it only reported how youth were misinterpreting his speeches. However, soon thereafter the Bangladesh Government banned the broadcast of Naik’s Peace TV channel. Hasanul Haq Inu, the Information Minister, reasoned that “Peace TV is not consistent with Muslim society, the Quran, Sunnah, Hadith, Bangladesh’s Constitution, our culture, customs and rituals”.

On 13 July 2016, Vishva Hindu Parishad leader Sadhvi Prachi announced a reward of ₹50 lakh (US$70,000) to anyone willing to behead Zakir Naik. This came a day after a Shia group styling itself the “Hussaini Tigers” placed a ₹15 lakh (US$21,000) bounty on his head.

In 2016, he admitted that Rahil Sheikh, involved in 2006 Mumbai train bombings was working as a volunteer for his organization Islamic Research Foundation (IRF) but he did not know Rahil personally. However, Naik also claimed that Rahil was removed from his office. Nearly 200 people lost their lives in the bombing attack and investigation revealed the bombers were influenced by Naik’s preachings.

On 18 July 2017, India revoked Naik’s passport following a recommendation from the National Investigation Agency (NIA). On 28 July 2017, the NIA declared Naik an offender and initiated a process to attach his assets. In December 2017, Interpol refused the Indian Government’s request to issue a red corner notice (RCN) against Naik. In January 2018, the Tribunal judge criticised the Enforcement Directorate for attaching Naik’s properties without mentioning any offenses in the chargesheet. The judge added: “In the last 10 years, the ED has done nothing to attach Asaram’s properties, but in the case of Naik, I can see the ED working with quite a bit of speed”.

In 2018, DVDs of Zakir Naik were recovered in raids on houses of accused in murder of Hindu Munnani leader C Sasikumar in Coimbatore.

In July 2019 Interpol refused for a third time to issue a Red corner notice against Naik after repeated requests by the Indian Government. Naik currently resides in Malaysia, where he has permanent resident status.

Naik delivered a speech on Islamophobia on 9 August 2019 at the Sultan Mohammad IV Stadium, Kota Bharu, Kelantan which was attended by more than 100,000 people.

On 11 May 2019, in an interview in Week magazine, Naik harshly criticized Narendra Modi and the BJP for what he called false charges and propaganda against him for political purposes, and said that he is targeted for his popularity. He stated that he would not return to India while Modi remained in power, according to the example of Muhammad in Hijrah. He also described Modi and the BJP as dangerous for Indian Muslims’ security, labelling Modi a “liar” and the “number one terrorist of India according to Google.” He also invited Modi to take part in a debate with him about Hinduism. In 2016, Naik had praised Modi, saying: “I am totally for him” because he was the first prime minister of India to have visited so many Muslim-majority countries.

Indian prime minister Narendra Modi slammed Zakir Naik in one of his electorial publicity visit in May 2019, saying that, Sri Lanka bombing was inspired by him and in spite of that the Congress supports Zakir Naik.

During a lecture Zakir Naik held on 8 August 2019 in Kota Bharu, Kelantan state, Malaysia, he said that Chinese people living in Malaysia are “old guests” who should return to China, suggesting they needed to be forcibly deported out of the country. In the same lecture, he also claimed that Hindus living in Malaysia had “100 times more rights” than the Muslim minority in India, and were more loyal to Indian PM Narendra Modi than to Malaysian PM Mahathir Mohamad. These comments sparked outrage across Malaysian society, being criticised as inciting racial and religious hatred and disrupting the peace and harmony between communities. By 15 August, four government ministers called for revocation of Zakir Naik’s permanent residency and for him to be extradited to India. Citizens lodged a total of 115 police complaints against Naik.

Naik claimed on 11 January 2020 that the Modi government approached him in September 2019 through an envoy and offered to provide him “safe passage” to India if he spoke in support of the government’s move to abrogate Article 370 in Jammu and Kashmir. In a 14 January 2020 tweet, Congress leader Digvijaya Singh asked Modi to clarify Naik’s claim of an offer of safe passage to India.