The quantum Hall effect is a macroscopic quantum phenomenon in a two-dimensional electron system. The two-dimensional electron system in SrTiO3 has sparked a great deal of interest, mainly because of the strong electron correlation effects expected from the 3d orbitals. Here we report the observation of the quantum Hall effect in a dilute La-doped SrTiO3-two-dimensional electron system, fabricated by metal organic molecular-beam epitaxy. The quantized Hall plateaus are found to be solely stemming from the low Landau levels with even integer-filling factors, ν=4 and 6 without any contribution from odd ν's. For ν=4, the corresponding plateau disappears on decreasing the carrier density. Such peculiar behaviours are proposed to be due to the crossing between the Landau levels originating from the two subbands composed of d orbitals with different effective masses. Our findings pave a way to explore unprecedented quantum phenomena in d-electron systems.