Transcranial magnetic stimulation (TMS) is used to modulate permeability of the blood brain barrier in a transient, safe and non-invasive manner. A conventional or deep TMS coil may be placed on a head in a vicinity of a tumor, for example. A series of magnetic pulses is provided to the brain with a tailored stimulation protocol. In one of many possible clinical applications, a pharmaceutical substance may be introduced during a time frame before, during or after providing the magnetic pulses to treat a tumor in the brain.