Biomedical Engineering Annual Salaries Nationally. According to the United States Department of Labor’s Bureau of Labor Statistics, biomedical engineers were paid a median annual salary of $84,670 in May 2011.Biomedical engineers in the bottom 10 percent were paid $51,380 a year or less.In addition, biomedical engineers in the top 10 percent were paid $134,150 or more, a salary that is more than twice the annual wage that workers in the bottom 10 percent received.ean annual salaries earned by biochemists and biophysicists in the industry were $206,600. The grant-making and giving-services industry paid the professionals a mean annual salary of $137,540, making it the second-highest-paying industry for biochemists and biophysicists.