Surface plasmon resonance (SPR) sensors are attracting considerable attention for their use in biomaterials inspection, chemical detection, and physical testing. This paper presents an experimental investigation on an SPR-based plastic optical fiber (POF) refractive index sensor. The sensor was fabricated using a POF in which some of the core was removed by polishing and a 40 nm gold thin film was deposited on the polished surface. The refractive index sensor was used to measure analytes with refractive indices in the range from 1.330 to 1.456. Two windows, an SPR window and a refraction window, were observed in the optical transmission spectrum, where the SPR window from 650 to 700 nm and the refraction window from 760 to 780 nm show a strong linear relationship between the SPR wavelength and the normalized transmitted intensity. Sensitivities of 328 nm/RIU and −0.83/RIU (RIU, refractive index unit) were achieved for the SPR and refraction windows, respectively. We also discuss the merits of both windows for biomolecule sensing.