Deep donor levels in ZnO single crystals doped with transition metal (TM; Co or Mn) were characterized by isothermal capacitance transient spectroscopy (ICTS) applied to ZnO-based Schottky junctions, Au/ZnO (0001) or Ag/ZnO (0001). The barrier height at the junction and donor concentration was not influenced by TM. A deep donor level at 0.28 eV was detected by ICTS; however, its energy dispersion and concentration was composition independent. The effect of doping with TM was found in the magnitude of leakage current; in other words, the leakage current at the Au/ZnO:Mn junction was lower than the other junctions on undoped or Co-doped crystals.