Rock discontinuities filled with soil-like materials commonly exist in rock masses, where the infill material is usually unsaturated, and the joint could have a much higher shear strength compared with fully saturated conditions. Understanding the shear behavior of unsaturated infilled joints is important when assessing ground stability such as in open cut mines or underground excavations. However so far, research on this topic is rare and not mature. This paper investigates the shear behaviour of unsaturated infilled joints in the numerical software FLAC. The FLAC soil-water retention and permeability models were modified in FISH subroutine to consider infill porosity change. A series of constant water content direct shear tests on infilled joints under various ratios of infill thickness to asperity height (t/a) were numerically conducted. Results highlight the necessity of correcting the intrinsic models in FLAC, and indicate that t/a ratio has a distinct influence on small-strain shear behaviour. Shear induced variations of fundamental infill parameters (e.g. matric suction, degree of saturation and saturated permeability) are discussed.