Robert Daniel, a part-time computer science instructor at Antelope Valley College, submitted his written resignation on Friday. He had taught at the university in Lancaster, about 50km north of Los Angeles, since August 2002.
He could not be reached for comment on Friday night.
Daniel had been under investigation by school officials after a Muslim student complained he ordered her to remove her headscarf or leave class on 18 February.
Fajr Burhan, 19, who was studying electrical engineering, said she was ordered to take off the scarf "the second I walked into the class."
Scarf 'blocks view'
Daniel told her that he did not permit headgear in class because it might block the view of other students.
Burhan said she told Daniel the hijab is "for a religious purpose" and "it's not something that I can just take off."
She then sat down without removing the scarf and Daniel became "very furious," Burhan told the Antelope Valley Human Relations Task Force on Monday night.
Interim President Jackie Fisher apologised and Burhan has been allowed to attend classes wearing the scarf.