A comprehensive thermophysical study of isomeric room-temperature ionic liquids n-butyl-3-methyl-pyridinium tetrafluoroborate and n-butyl-4-methyl-pyridinium tetrafluoroborate has been performed. This paper reports various experimental data including density, speed of sound, refractive index, surface tension, isobaric molar heat capacity, and kinematic viscosity. From the experimental results, coefficients of thermal expansion, dynamic viscosities and molar refractions of the studied ionic liquids have been determined. Results have been analyzed paying special attention to the different features of the isomers and their structural differences. Several theories and empirical relations have been applied in order to predict physical properties of ionic liquids. A good agreement between experimental and calculated data has been found. Furthermore, a study about the versatility and application of the different relationships has been carried out finding that in general density and coefficients of thermal expansion can be estimated with relatively good accuracy.