We report a microfluidic fiber-optic refractive index (RI) sensor based on an in-line Fabry-Perot (FP) interferometer, which is formed by a silica tube sandwiched by two microstructured fibers (MFs). The sensor reported here can be fabricated at low cost, possess a robust structure, and has microfluidic capability. The micro-sized holes in the MFs naturally function as microfluidic channels through which liquid samples can be efficiently and conveniently delivered into and out of the FP cavity by a pressure/vacuum pump system for high-performance RI measurement. Due to the microfluidic capability enabled by the MFs, only sub microliter sample is required. We also experimentally study and demonstrate the superior performances of the sensor in terms of high RI sensitivity, good measurement repeatability, and low temperature cross-sensitivity.