Doping with 3d transition metals, particularly Mn, is thought to play an important role in determining the reliability of dielectrics used in multi-layer ceramic capacitors (MLCCs). However, a detailed examination of the electronic structure, solution energies and compensation mechanisms of these systems is lacking. In this paper, the quantitative analysis of the substitution of Mn in perovskite-type BaTiO3 using first-principles calculations in combination with chemical thermodynamics is reported. The solution energies of dopants with vacancy and n-type and p-type charge compensations have been systematically calculated. Substitution onto the two crystallographically different cation sites in cubic BaTiO3 under four different thermodynamic conditions with different chemical potentials is also examined. Mn is found to be stable on Ti sites under all conditions examined, although its charge state varies. In the oxidizing limit, Mn substitutes for Ti as a Mn4+ ion, but in the reducing limit, Mn substitutes for Ti as a Mn2+ ion compensated by the formation of an O vacancy. Depending on the Fermi level of the system, the valence state of Mn varies from Mn4+ under p-type conditions, to Mn2+ under n-type conditions. Mn3+ is not found to be stable. These results agree well with the experimentally determined site preferences and valence states of Mn, and help to further elucidate the features of Mn-doped BaTiO3 at the atomic level.