First-principles spin-polarized calculations have been conducted to investigate the structural, electronic and magnetic properties of 3d transition metal Mn doping into two typical sites in the upper layer of bilayer graphene with the AB Bernal structure. One of the doping sites is above the center of a carbon hexagon of the lower graphene layer (called the H site) and the other is directly on top of a carbon atom of the lower graphene layer (called the T site). We found that Mn doping enlarges the interlayer distance in bilayer graphene. Charge density distribution indicates that the region between the upper and lower graphene layer has apparent covalent-bonding characters due to the Mn doping. In the spin-polarized band structure of H site doping, the π and π(*) bands separate from each other at the Dirac point both in majority spin and minority spin. In the band structure of T site doping, the Fermi level is located above the Dirac point and moves to the conduction bands in majority spin and minority spin, making the bilayer graphene n doped. A high spin polarization of 95% is achieved due to the H site doping. The local moment of Mn for H and T site doping is reduced to 1.76 μ(B) and 1.88 μ(B), respectively, which are smaller than the value (5 μ(B)) in the free state.