It's his second attempt to fill the post.
This time, he's picked Judge Joe R. John Sr. who served on the NC Court of Appeals from 1992-2000, as Resident Superior Court Judge from 1984 until 1992 in Greensboro, and as District Court Judge in 1980 until 1984.
"This is a complex job and I’m pleased that Judge John has agreed to serve," Cooper said in a statement.
John replaces former Chief Judge of the North Carolina Court of Appeals Gerald Arnold - who Cooper named to the post in September.
Arnold later said he couldn't serve saying he wouldn't be able to handle a job with such a large time commitment.
Problems at the SBI have been the subject of media reports for months. In August, a report by independent investigators found that SBI agents helped prosecutors obtain convictions over a 16-year period by misrepresenting blood evidence and keeping critical notes from defense lawyers.
The audit revealed that as many as 190 cases may have been affected.
Cooper said John will oversee a team of lawyers who are reviewing the reporting policies and procedures used by the SBI lab to ensure that information is properly shared with prosecutors and defendants.
He will also oversee day-to-day operations while a national search for a permanent lab director continues.