With the resignation of Mike Ward, the Superintendent of Public Instruction race was the only 2004 Council of State contest in which there was no incumbent; consequently both major parties saw contested primaries. On the Republican side, former Wake County board of education member Bill Fletcher easily bested retired professor Jeanne Smoot. The Democratic primary between state Department of Instruction official June Atkinson, North Carolina Board of Education member J. B. Buxton and state agricultural education coordinator Marshall Stewart led to a second primary. Stewart polled narrowly ahead of Atkinson in the first primary, but failed to capture the 40% support needed to take the nomination. In a statewide runoff primary, Atkinson captured the Democratic nomination.
The race, along with the race for Agriculture Commissioner (see below) was caught up for nearly a month in a statewide recount because of the narrow margin. Fletcher argued that provisional ballots, required under the Help America Vote Act of 2002 for federal races, were improperly counted in state races under North Carolina law. However, on 30 November 2004, the State Board of Elections certified Atkinson the winner. Fletcher appealed the recision to the North Carolina Supreme Court. Atkinson, in turn, petitioned the North Carolina General Assembly to resolve the disputed election. On August 24, 2005, the General Assembly met in a joint session to vote on the disputed election, as the state constitution called for. Atkinson won this vote and was sworn-in that afternoon.
The election of the Superintendent of Public Instruction was the last American election from 2004 to be decided. 
Because of the loss of about 4,000 votes in Carteret County, North Carolina, the race for State Agriculture Commissioner could not be resolved for several months. Although the North Carolina Board of Elections certified the close race for State Superintendent of Public Instruction on 30 November 2004, they reached an impasse on the Agriculture Commissioner Race, splitting 3-2 in favor of calling a new statewide election for the seat over calling a new election in Carteret County alone; 4 votes would have been required to take action on either option.
In early December, the North Carolina Board of Elections ordered a new election for January 11, 2005, in Carteret County alone, for voters whose ballots had been lost or who had not voted in the November 2 election. Both candidates appealed the decision, Cobb arguing that a statewide revote should be held, Troxler arguing that a revote should be limited to those voters whose votes were lost. A Wake County superior court judge overturned this decision on December 17, calling it "arbitrary and capricious" and "contrary to law," requiring the State Board of Elections to revisit the issue.
On December 29, the State Board of Elections ordered a new statewide election for the post. On January 13, 2005, the superior court invalidated this order as well, and sent the contest back to the Elections Board for resolution. Following this ruling, Cobb conceded defeat. On February 4, the State Board of Elections officially certified Troxler as the winner of the 2004 election.