According to one embodiment, a method for manufacturing a magnetic recording medium includes forming patterns having protrusions and recesses of a ferromagnetic material onto a recording track section and a servo section on a substrate, forming a flattening film, a top surface of which is higher than that of the protrusion of the ferromagnetic material, onto the ferromagnetic material, and performing ion beam etching onto the flattening film up to a top surface of the protrusion of the ferromagnetic material, and determining an end point of flattening etching on the basis of a change in the total number of incident particles by means of an ion counter installed so as to be at an angle θ with respect to a perpendicular direction to the substrate in accordance with a material of the flattening film.