A magnetorheological elastomer (MRE) is a smart material that has a reversible and variable modulus in a magnetic field. Natural rubber, which has better physical properties than silicone matrices, was used as a matrix in the fabrication of the MREs used in this study. Carbonyl iron powder (CIP), which has a rapid magnetic reaction, was selected as a magnetic material to generate the magnetic-field-dependent modulus in the MREs. The MRE specimens were cured in an anisotropic mold, which could be used to induce a uniaxial magnetic field via permanent magnets, to control the orientation of the CIP, and the shear modulus of the MREs was evaluated under a magnetic field induced by using a magnetic flux generator (MFG). Because the use of a conventional evaluation system to determine the magnetic-field-dependent shear modulus of the MREs was difficult, an evaluation system based on single degree-of-freedom vibration and electromagnetics that included an MFG, which is a device that generates a magnetic field via a variable induced current, was designed. An electromagnetic finite element method (FEM) analysis and design of experiments (DoE) techniques were employed to optimize the magnetic flux density generated by the MFG. The optimized system was verified over the range to determine the magnetic flux density generated by the MFG in order to use a magnetic circuit analysis to identify the existence of magnetic saturation. A variation in the shear modulus was observed with increasing CIP volume fraction and induced current. The experimental results revealed that the maximum variation in the shear modulus was 76.3% for 40 vol% CIP at an induced current of 4 A. With these results, the appropriate CIP volume fraction, induced current, and design procedure of the MFG can be proposed as guidelines for applications of MREs based on natural rubber.