Jonathan Elmer (November 29, 1745 – September 3, 1817) was an American politician, of the Pro-Administration (Federalist) Party.
Elmer was born in Cedarville, New Jersey, in 1745. He was graduated from the University of Pennsylvania in 1769 after studying medicine. He practiced medicine in Bridgeton, New Jersey, until he became sheriff of Cumberland County in 1772. Physically frail, during the American Revolutionary War he was a militia officer but apparently did not see active duty.
Elmer was a delegate to the Continental Congress three times: 1777 to 1778, 1781 to 1783, and 1787 to 1788. In 1780 and 1784 he represented Cumberland County in the New Jersey Legislative Council. The College of New Jersey (now known as Princeton University) made Elmer a trustee in 1782. He served in that position until 1795. The New Jersey Legislature appointed Elmer to the United States Senate for the term of March 4, 1789 to March 4, 1791. His health declined after that, and Elmer died in 1817, and he was interred in Old Broad Street Presbyterian Church Cemetery in Bridgeton.
Elmer's younger brother, Ebenezer Elmer, and Ebenezer's son Lucius Elmer were members of the United States House of Representatives.