Atabani is married to Samia Yousif Idris Habbani, the daughter of a renowned tribal chief in Sudan; she is also a medical doctor who held the post of Social Affairs Minister in the Government of Khartoum State.
On his return to Sudan he became a lecturer at his alma mater, the Faculty of Medicine, University of Khartoum.
When South Sudan gained its independence in 2011, the government in Khartoum lost some 70% of its annual revenue from the oil industry, which is located mostly in the South, and by the summer of 2013, the government was forced to make cuts in public spending to accommodate its reduced budget.
Atabani was the lead-signatory among 31 reformers who sent a memorandum to the president, deploring the killings and advising a different response the situation.
In October 2013, the 31 signatories, led by Atabani, announced that they were resigning from the NCP, to found a new party.