Cordyceps militaris (C. militaris) is a unique and valuable medicinal fungus belonging to the Cordyceps species. C. militaris is the only fungus that contains cordycepin which is a biologically active compound. In previous studies, light-emitting diodes (LEDs) are known to be effective in increasing cordycepin content, but metabolic profiling of LED-stimulated C. militaris has not been confirmed. Metabolic profiling is essential to understanding the metabolic regulation of cordycepin. This study studied the physiologically active secondary metabolites of C. militaris according to the presence or absence of stimulation of LEDs through GC-MS analysis. Most of the metabolites were detected in both samples, but there was a clear difference in the detected concentration. In particular, C. militaris had a significant difference in amino acid levels when stimulated with LEDs. Our results suggested that LEDs could stimulate amino acid synthesis in C. militaris mycelium to increase the cordycepin content.