Naked barley grains were germinated at 25 °C for 12, 24, and 36 h, followed by infrared or hot air drying. Effects of germination and drying treatments on the composition and content of phenolic compounds in naked barley were investigated using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The results revealed that germination of naked barley induced significant changes in the profile of phenolic compounds depending on germination period. Also, the content of phenolic compounds significantly increased (P < 0.05) as the germination prolonged to up to 36 h. Furthermore, significantly greater retention of phenolic compounds was found after the infrared drying of germinated naked barley than that found after hot air drying. Phenolic compounds of the raw and germinated/dried naked barley samples could be differentiated independently by partial least squares discrimination analysis (PLS-DA). The obtained results suggest that germination and infrared drying are promising processing methods for producing germinated naked barley rich in flavonoids with potential health benefits.