The University of Aden employed bin Habtour as a prorector from 1994 to 2001. In 2001, President Ali Abdullah Saleh named bin Habtour to serve as Deputy Minister of Education, an office he held until 2008. Afterward, he became president and rector of the University of Aden. President Hadi appointed bin Habtour as Governor of Aden by decree on 22 December 2014. He was sworn three days later. As Aden's new governor, he confronted the unrest created by the Houthitakeover in 2015, including a pro-separatist uprising in Aden seaport. He also met with Hadi after he fled to Aden from the capital of Sana'a. At some point during the months-long battle for Aden in 2015, bin Habtour fled the city. In July, the Yemeni government-in-exile in Saudi Arabia announced the appointment of his former deputy, Nayef al-Bakri, as governor.
Premiership
On 2 October 2016, he was appointed as Prime Minister by the Houthis. On 4 October, he formed his cabinet. The cabinet, which includes members of the Southern Movement, is not internationally recognized. On 28 November 2016, a new cabinet was formed. Ansarullah and the General People's Congress announced a government of national salvation to be led by Habtour. He then said that the new coalition would be a vital step towards re-organizing Yemen's internal affairs and dealing with the consequences of the Saudi Arabian-led intervention in Yemen. However, the UN Special Envoy for YemenIsmail Ould Cheikh Ahmed said the move was "a new and unnecessary obstacle. Yemen is at a critical juncture. The actions recently taken by Ansarullah and the General People's Congress will only complicate the search for a peaceful solution. The parties must hold Yemen’s national interests above narrow partisan ambitions and take immediate steps to end political divisions and address the country’s security, humanitarian and economic challenges." He further claimed that such an action could harm peace talks. On 13 December 2016, he accused United Kingdom of war crimes against Yemen, by giving bombs to the Saudi-led coalition. On 5 April 2017, he tendered his resignation as Prime Minister by submitting it to the Supreme Political Council, according to sources close to him. This occurred after Houthi militiamen stormed the headquarters of the General Authority for Social Security and Pensions in Sana'a, reportedly taking over the establishment and seizing funds intended for pensioners.