After completing her doctorate, she spent four years at Yale University as a postdoctoral associate in the Department of Molecular Biophysics and Biochemistry. From Yale, Trewhella moved to Los Alamos National Laboratory in 1984 and held various roles there over a twenty-year period. In 1999 she was named a laboratory fellow. She was the first woman to earn the honor. By 2003 she was Bioscience Division Leader and Program Manager for the Department of Energy Office of Biological and Environmental Research. She was consulted by press and the United States government about bioterrorism during the 2001 anthrax attacks. She held an adjunct associate professorship at the University of New Mexico.