There is a dense group of OB and Wolf-Rayet stars within a fraction of a parsec from the super-massive black hole (SMBH) at the Galactic Center. These stars appear to be coeval and relatively massive. A subgroup of these stars orbits on the same plane. If they emerged with low to modest eccentricity orbits from a common gaseous disk around the central super-massive black hole, their inferred lifespan would not be sufficiently long to account for the excitation of their high orbital eccentricity through dynamical relaxation. Here we analyze the secular perturbation on Galactic Center stars by an intermediate-mass companion (IMC) as a potential mechanism to account for these young disk stars high eccentricity. This IMC may be either an intermediate-mass black hole (IMBH) or a compact cluster such as IRS-13E. If its orbital angular momentum vector is anti-parallel to that of the disk stars, this perturbation would be effective in exciting the eccentricity of stars with orbital precession rates which resonate with IMCs precession rate. If it orbits around the SMBH in the same direction as the disk stars, the eccentricity of the young stars can still be highly excited by the IMC during the depletion of their natal disk, possible associated with the launch of the Fermi bubble. In this scenario, IMCs precession rate decreases and its secular resonance sweeps through the proximity of the young stars. We carry out numerical simulations with various inclination angles between the orbits of IMC and the disk stars and show this secular interaction is a robust mechanism to excite the eccentricity and inclination of some disk stars.