Methods and systems are disclosed for treatment of nail disease in a patient. A system (10) includes a light applicator (12) operable to irradiate a nail having a nail disease with light that includes a wavelength corresponding to an absorption spectrum of the nail disease and a duty cycle with a series of alternating light emissions (22) and pauses, a light source (14) coupled with the light applicator (12) for supplying the light to the light applicator (12), and a controller (16) coupled with the light source(14) for controlling the operation of the light source (14) such that the pauses are timed for movement of the light applicator (12) between light emissions (22).
