The name Jonathan comes from the Hebrew name יוֹנתן‎ (yōnāṯān), short for יהוֹנתן (yǝhōnāṯān). It is a theophoric name that comes from the combination of the abbreviation of the name of the Hebrew God, יהו (Yahw(eh), sometimes shortened to just יו), and the Hebrew verb נתן (naṯan, pronounced na-THAN), meaning "to give," meaning "Yahw(eh) has given."

Perhaps the most famous Jonathan in the Bible is the son of King Saul, who famously pledged his love (and the throne of Israel) to his best friend, David in 1 Samuel 20:16–17: "Thus Jonathan made a covenant with the house of David, saying, 'May the LORD seek out the enemies of David.' Jonathan made David swear again by his love for him; for he loved him as he loved his own life." Moses also had a grandson named Jonathan, who set up an idol for the tribe of the Dan and served them as priest along with his sons in Judges 18:30. This passage is famous for later redactors emending the text reading "Moses" to "Manasseh," to keep a descendent of Moses from being a leading idolator.