A finite-difference-time-domain (FDTD) approach is undertaken to investigate the extraordinary optical transmission (EOT) phenomenon of Au circular aperture arrays deposited on a Bragg fiber facet for refractive index (RI) sensing. Investigation shows that the choice of effective indices and modal loss of the Bragg fiber core modes will affect the sensitivity enhancement by using a mode analysis approach. The critical parameters of Bragg fiber including the middle dielectric RI, as well as its gap between dielectric layers, which affect the EOT and RI sensitivity for the sensor, are discussed and optimized. It is demonstrated that a better sensitivity of 156 ± 5 nm per refractive index unit (RIU) and an averaged figure of merit exceeding 3.5 RIU-1 are achieved when RI is 1.5 and gap is 0.02 μm in this structure.