This invention provides a non-invasive system for measuring pain level in a body at a site containing a predetermined concentration of magnetic nanoparticles. A drive coil and a pickup coil transmit and measure a field passing through the site based upon response of the magnetic nanoparticles, and a processor computes a pain level based upon variations in the field. The pain level can be indexed to an absolute scale that affords more predictability and objectivity in determining true pain level. Illustratively, the processor derives values for levels of cytokine IL-6, SP and temperature at the site, which are translated into the pain level. In an embodiment, the system and method can be implemented in a handheld device in which the drive coil and pickup coil reside in a housing.