Khan, 76, recently formed the Tehrik-e-Tahaffuz Pakistan party and held talks with political leaders about forming alliances for the polls that will mark the first democratic transition in Pakistan's history.
"Doctor Abdul Qadeer Khan will not take part in the election but he will continue to support his party and its allies," TTP spokesman Rohail Akbar said.
"The party's candidates and our allies have obtained nomination papers and they will stand for election," he said.
He has said the party will focus on issues like corruption, inflation and an energy crisis during its campaign.
The scientist was placed under house arrest in 2004 after he confessed to running a clandestine nuclear proliferation ring.
He later retracted his confession and authorities eased restrictions on him in 2009.