The LEDs in a phototherapy LED pad are controlled so that the intensity of the light varies in accordance with a sinusoidal function, thereby eliminating the harmonics that are generated when the LEDs are pulsed digitally, in accordance with a square-wave function. This is accomplished analogically by using a sinusoidal wave to control the gate of a MOSFET connected in series with the LEDs or by using a digital-to-analog converter to control the gate of the MOSFET with a stair step function representative of the values of a sinusoidal function at predetermined intervals. Alternatively, pulse-width modulation is used to control the gate of the MOSFET in such a way that the average current through the LEDs simulates a sinusoidal function. In additional to using a simple sine wave function, the LED current may also be controlled in accordance with “chords” containing multiple sine waves of different frequencies.