Disclosed herein is a method for treating a brain disease in which focused ultrasound and magnetic targeting are applied to a subject in need of such treatment, so that therapeutic agent-magnetic nanoparticle composites are directed across the blood-brain barrier to a designated locus inside the brain of the subject. Each of the composites includes a magnetic nanoparticle that is formed of an iron-based core and a shell encapsulating the iron-based core, and a therapeutic agent that is bound to the shell of the magnetic nanoparticle. The magnetic nanoparticle has a size ranging from 5 to 200 nm. The iron-based core has a crystalline structure that imparts the composites with a sufficiently high magnetization, thereby enhancing magnetic targeting of the composites to the designated locus inside the brain of the subject. The magnetic targeting treatment is conducted via a magnet providing a magnetic flux density not less than 0.18 T.