In this paper, the structural design and experiment of MEMS resonators for accurately measuring Young’s modulus is described. To establish an accurate measurement technique for the Young’s modulus of nanometer-thick thin films, first, we design MEMS resonators that can accurately derive the Young’s modulus of a structural material. The designed resonators are fan-shaped and can vibrate sympathetically in-plane. In total, the shape and dimensions of eleven mechanical parts in a resonator are considered using finite element (FE) analyses, and it is shown that the thickness-to-width ratio and the length of the rotation support beam affect the derivation of Young’s modulus. After device design, we fabricate the resonators made of single-crystal Si (SCS) using three different etching techniques: Bosch process deep reactive ion etching (DRIE), non-Bosch DRIE, and focused ion beam (FIB) etching. When the resonators fabricated by non-Bosch DRIE and FIB etching are used, experimentally obtained Young’s moduli are comparable to FE-analyses-derived Young’s moduli. The resonators with a long rotation support beam and a large thickness-to-width ratio of the beam can provide Young’s moduli that are close to the ideal value. However, Young’s moduli obtained from the resonators fabricated by the Bosch process DRIE differ largely from FE-analyses-derived Young’s moduli. The sidewall effect is discussed in the light of the modal analyses by the FE method.