Israeli media reported that the assailants poured flammable liquid into the bathroom window before lighting it and fleeing the scene.
The Orthodox seminary is located near Jaffa Gate.
“Jesus is a son of a whore” and “Redemption of Zion” were sprayed on the walls.
On Tuesday, extremist Jewish settlers set fire to a mosque in the southern West Bank town of al-Jaba west of Bethlehem, locals told Ma’an.
The Palestinian foreign ministry said the attack was tantamount to “an official declaration of religious war,” the official WAFA news agency reported.