Light is an important factor for cordycepin production in Cordyceps militaris. We investigated the effects of different light-emitting diode (LED) conditions including various LED wavelengths and their combinations on cordycepin production in Cordyceps militaris cultivated in submerged culture. The results of our study showed that the combinations of LED wavelengths were more beneficial than single LED sources for cordycepin production. Among the three tested wavelength combinations, the greatest effects for cordycepin production were observed for the red:blue light combination at the wavelength ratio of 5:5 or 3:7. The optimal culture conditions were 19.2278 h/day of illumination time; 9.19497 g/50 mL of glucose content in the media; and 53.112 h of cultivation time. Our model predicted a maximum yield of 2860.01 μg/mL cordycepin. Finally, to verify the calculated maximum, we performed experiments in the culture media representing the obtained optimum combination and the cordycepin yield of 2412.5 μg/mL.