Owaisi belongs to the Hyderabad-based All-India Majlis-e-Ittehadul Muslimeen (AIMIM) party, of which his father and grandfather have been presidents. The party, while opposed to jihadist terrorism, still practises a politics of "competitive chauvinism," according to journalist Kingshuk Nag.
Owaisi made his political debut in 1994 in the Andhra Pradesh Legislative Assembly election. Contesting from the Charminar constituency which his party has been winning since 1967, he defeated his nearest rival a breakaway party Majlis Bachao Tehreek's candidate by a margin of 40 thousand votes. He succeeded Virasat Rasool Khan as the elected representative from the constituency. In the 1999 election, he defeated his nearest rival Telegu Desam Party candidate Syed Shah Noorul Haq Quadri by 93 thousand votes. Owaisi was polled 126 thousand votes in the election. In 2004 election, he was succeeded by Syed Ahmed Pasha Quadri as the member of the Assembly from the constituency.
In 2004, Owaisi's father Sultan Salahuddin Owaisi who had been representing the Hyderabad constituency in the Lok Sabha (lower house of Indian parliament) refused to contest further citing poor health. The constituency has 70% Muslim population. He was polled 38% votes compared to his nearest rival Subhas Chanderji's 28%.
In 2008, the Left Front (which consisted of Communist Parties) withdrew their support to the central government of India which was led by the United Progressive Alliance. This was done in response to Indo-US nuclear deal signed by Indian Prime Minister Manmohan Singh and US President George W. Bush which allowed India to keep nuclear bombs but in return had to allow international inspection. The Communist parties felt that by this deal, India would become a pawn of the United States. Due to the Left Front withdrawing support, a vote of confidence was held in Indian Parliament. When Uttar Pradesh chief minister Mulayam Singh Yadav claimed that Muslims of India opposed the deal, Owaisi said that it was an attempt to give a communal angle to the deal. Owaisi announced his support for the United Progressive Alliance in the vote of confidence. He claimed that his top priority was to prevent the opposition right wing Bharatiya Janata Party to ascend to power and to prevent Lal Krishna Advani from becoming the country's Prime Minister. He further stated:
We will express our reservations on the foreign policy impact but at no cost would we like to see the BJP coming in to power, at no cost we would like to see Mr Advani, who is an accused in Babri Masjid demolition case becoming the prime minister of this great nation, thereby destroying the future of Muslims and weakening the secularism.
In the 2009 Indian general election, Zahid Ali Khan, the editor-in-chief of an Urdu daily The Siasat Daily was pitted against Owaisi. He was supported by rival Telegu Desam Party, Telangana Rashtra Samithi, Communist Party of India, Communist Party of India (Marxist). Hindustan Times wrote that the AIMIM party faced "tough challenge" in the Hyderabad constituency. However, Owaisi emerged victorius and defeated Ali Khan by a margin by 110 thousand votes. He increased the winning margin by 10 thousand votes as compared to 2004 election.
Owaisi was awarded the 2014 Sansad Ratna award (Gem of parlamentiarians) October 2013 for his performance in the 15th session of Indian parliament. During this period, he asked 1080 questions in the Parliament compared to the national average of 292. His attendance at 70% was 6% short of the national average. The Milli Gazette wrote that he "has gained wide respect nationally among Indian Muslims for his bold speeches in Lok Sabha (lower house of Indian parliament)". He took up issues in the Parliament which pertained to the interests of the minority community. Also when he raised the issue of waqf properties in the parliament, the then Rural Development Minister Jairam Ramesh confessed that it was a fault of his ministry in recognising waqf as a serious matter.
In April 2014, Owaisi filed his nomination for the Hyderabad constituency in the 2014 general election. He declared movable assests worth 2.7 million rupees (around $ 42,000) and immovable assests worth 30 million rupees (around $ 463,000). He was elected from the constituency once again by defeating his nearest rival Bharatiya Janata Party's Bhagvanth Rao by a margin of 197 thousand votes.
Owaisi announced that his party AIMIM would contest the Bihar Legislative Assembly election, 2015 from mainly from the Muslim dominated area of Seemanchal region of the state. News18 India wrote that the party candidates would divide votes and the voters suspected him of being an agent of the Hindu nationalist Bharatiya Janata Party. He said that he was realistic about their chances of winning. He claimed that the Seemanchal region was underdeveloped and he blamed Bihar's Chief Minister Nitish Kumar, Indian National Congress party and Bharatiya Janata Party for it. He said that his aim was to pressurise the government to create a regional developmental council for the region. Although the party contested from six constituencies of Seemanchal region, it failed to win any seat.