Almost 350 students have signed an online petition to see Jerusalem return to the college's list of hymns for the current term.
While principal George Hartley stressed the 'stirring and uplifting' hymn had not been banned from the college, he confirmed it had not be included in the schedule of assembly hymns for this term.
He explained this was because the college wanted pupils to be familiar with a broad range of hymns and not just a small number which were simply repeated every term.
But on the petition, student Charlie Brewin said: 'On behalf of all the students of Elizabeth College, I think I can safely say that we would like it back.
'We will not cease from mental fight; nor shall our swords sleep in our hands until Jerusalem is reinstated as a college hymn, as it should be.
'Over the years, Jerusalem has become a favourite of students to sing, and they show it with a notable increase in enthusiasm and volume when singing this hymn. It has become as close to our hearts as the college's Carmen.'