Emerson was relegated to the backbench following the 2004 Australian federal election, having supported Simon Crean and Mark Latham in leadership ballots against the wishes of his Right faction in Queensland.

While on the backbench he wrote a book, Vital Signs, Vibrant Society, proposing new economic and social policies for the Federal Parliamentary Labor Party.

[5][6] In March 2013, in a further reshuffle of ministerial responsibilities, Emerson gained an additional portfolio as Minister for Tertiary Education, Skills, Science and Research.

[7] However, after a leadership change in the federal Australian Labor Party in June 2013 in which Kevin Rudd took over as prime minister from Gillard, Emerson resigned his ministerial portfolios and said he would not contest his seat at the next election.

[8] Following the Australian federal election held a few months later in September 2013, Jim Chalmers took over from Emerson as the MP for the seat of Rankin in Queensland.

He was also a member of the CEDA Council on Economic Policy and chair of the advisory board, Centre for Transformative Innovation, Swinburne University of Technology.

[13] On the subject of Australia-China relations, Craig Emerson consistently argued prior to 2022 that the poor relationship was partly caused by Australia.

[14] In September 2023, Emerson led The Australian delegation of the resumed High Level leadership Dialogue to Beijing, where he also met with China's foreign minister Wang Yi.

[15] Emerson and former South Australian premier, Jay Weatherill, assisted by Lenda Onsalem, John Graham and senators Anthony Chisholm and Linda White, conducted the ALP's review of the 2019 federal election loss.

[17] Emerson was also a panellist assisting Greg Combet and Lenda Onsalem in the review of Labor's successful 2022 election campaign.