A method of manufacturing a magnetic recording medium is provided. The method includes: forming a magnetic layer 2 on a non-magnetic substrate 1; forming a mask layer 3 on the magnetic layer 2; forming a resist layer 4 which is patterned into a predetermined shape on the mask layer 3; patterning the mask layer 3 into a shape corresponding to the resist layer 4 using the resist layer 4; patterning the magnetic layer 2 into a shape corresponding to the mask layer 3 using the patterned mask layer 3; and removing the mask layer 3 that remains on the magnetic layer 2 by reactive plasma etching. The reactive plasma etching is performed under an atmosphere containing an organic compound having at least one kind or plural kinds of functional groups selected from a hydroxyl group, a carbonyl group, a hydroxy carbonyl group, an alkoxy group, and an ether group.