The dynamic analysis of fluid-conveying functionally graded pipes under two cases of temperature distributions is investigated in this study. Two cases of temperature distribution of functionally graded pipes are considered: warmer outside than inside in Case 1 and warmer inside than outside in Case 2. The purpose is to determine the effect of two cases of temperature distributions on the natural frequencies and the critical flow velocity by applying a conventional finite element of functionally graded pipes neglecting shear deformation. The numerical results show that the difference in the natural frequencies or the critical flow velocity between two cases of temperature distributions is not monotonic, and not always greater than 0, which is conditional on the volume fraction index and temperature gradient. The article indicates that the physical parameters of temperature-dependent functionally graded pipes should be selected to adapt for Case 1 and Case 2, respectively.