Ebenezer Elmer (August 23, 1752 – October 18, 1843) was an American physician from Bridgeton, New Jersey. He represented New Jersey in the U.S. Congress from the Democratic-Republican Party from 1801 to 1807. Elmer's older brother, Jonathan Elmer, and Ebenezer's son Lucius Elmer were members of the United States House of Representatives.