The atomic structures and electronic properties of isolated Mo atoms in bilayer epitaxial graphene (BLEG) on 4H-SiC(0001) are investigated by low temperature scanning tunneling microscopy (LT-STM). LT-STM results reveal that isolated Mo dopants prefer to substitute C atoms at α-sites and preferentially locate between the graphene bilayers. First-principles calculations confirm that the embedding of single Mo dopants within BLEG is energetically favorable as compared to monolayer graphene. The calculated band structures show that Mo-incorporated BLEG is n-doped, and each Mo atom introduces a local magnetic moment of 1.81 μB into BLEG. Our findings demonstrate a simple and stable method to incorporate single transition metal dopants into the graphene lattice to tune its electronic and magnetic properties for possible use in graphene spin devices.