The main difference between NADH and FADH2 is that NADH is a coenzyme composed of nicotinamide and adenine while FADH2 is a coenzyme composed of flavin adenine dinucleotide. NADH functions in the transfer of electrons from one molecule to another in redox reactions while FADH2 functions in the transfer of electrons from flavoproteins to CoQ in the electron transport chain.