A method of manufacturing a glass substrate for a magnetic disk is provided, by which polishing accuracy on an inner circumferential end face of a glass substrate is improved, and a thermal asperity trouble can be avoided. In a method of manufacturing a glass substrate for a magnetic disk, by which an inner circumferential end face of a cylindrical polishing object 12 is polished, the polishing object including a plurality of glass substrates 20 stacked on one another, a plurality of polishing cloths disposed around a rotation axis of an inner circumference polishing section having the rotation axis are contacted to the inner circumferential end face 116 of the polishing object at even pressure, then a polishing liquid is supplied between the inner circumferential end face of the polishing object and the inner circumference polishing section, and then the inner circumference polishing section and the polishing object are relatively rotated/moved with the rotation axis as a center, or relatively moved in a direction of the rotation axis, thereby the inner circumferential end face of the polishing object is polished.