The propagation characteristics of a surface acoustic wave (SAW) that travels along the surface of a solid object can vary significantly depending on the surrounding environment. SAW devices are employed in sensors that measure many different kinds of environments and their changes. This paper discusses a SAW sensor used to measure the concentration of methanol, a fuel required by methanol fuel cells. The permittivity of methanol exhibits significant variation depending on the concentration and the temperature. Two SAW resonators were used to measure the permittivity of a liquid; one with the cavity surface as an electrically open circuit, and the other short-circuited. Two resonating systems were constructed from an amplifier and a SAW resonator, and fluid was allowed to run through the cavities of the two resonators to measure the difference in the oscillation frequency. This difference in frequency changed in proportion to the permittivity of the liquid, so that its concentration could be measured. It was also experimentally demonstrated that the use of SAW resonators can stabilize measurements and improve reproducibility. A sensing system made of liquid flow cells and SAW sensors was then proposed. The proposed system is able to measure the real time concentration of methanol independently of the temperature and with good reproducibility.