This research article proposes and numerically investigates a photonic crystal fiber (PCF) based on a surface plasmon resonance (SPR) sensor for the detecting refractive index (RI) of unknown analytes. The plasmonic material (gold) layer is placed outside of the PCF by removing two air holes from the main structure, and a D-shaped PCF-SPR sensor is formed. The purpose of using a plasmonic material (gold) layer in a PCF structure is to introduce an SPR phenomenon. The structure of the PCF is likely enclosed by the analyte to be detected, and an external sensing system is used to measure changes in the SPR signal. Moreover, a perfectly matched layer (PML) is also placed outside of the PCF to absorb unwanted light signals towards the surface. The numerical investigation of all guiding properties of the PCF-SPR sensor is completed using a fully vectorial-based finite element method (FEM) to achieve the finest sensing performance. The design of the PCF-SPR sensor is completed using COMSOL Multiphysics software, version 1.4.50. According to the simulation results, the proposed PCF-SPR sensor has a maximum wavelength sensitivity of 9000 nm/RIU, an amplitude sensitivity of 3746 RIU−1, a sensor resolution of 1 × 10−5RIU, and a figure of merit (FOM) of 900 RIU−1in the x-polarized direction light signal. The miniaturized structure and high sensitivity of the proposed PCF-SPR sensor make it a promising candidate for detecting RI of analytes ranging from 1.28 to 1.42.