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Functionally graded materials (FGM) eliminate the stress singularity in the interface between two different materials and therefore have a wide range of applications in high temperature environments such as engines, nuclear reactors, spacecrafts etc. Therefore, it is essential to study the mechanical properties of different FGM materials. This paper aims at establishing a method for modelling FGMs in molecular dynamics (MD) to get a better insight of their mechanical properties. In this study, the mechanical characteristics of Cu-Ni FGM nanowires (NW) under uniaxial loading have been investigated using the proposed method through MD simulations. In order to describe the inter-atomic forces and hence predict the properties properly, EAM (Embedded atom model) potential has been used. The nanowire is composed of an alloying constituent in the core and the other constituent graded functionally along the outward radial direction. Simple Linear and Exponential functions have been considered as the functions which defines the grading pattern. The alloying percentage on the surface has been varied from 0% to 50% for both Cu-cored and Ni-cored nanowires. All the simulations have been carried out at 300 K. The L/D ratios are 10.56 and 10.67 for Cu-cored and Ni-cored NWs, respectively. This study suggests that Ultimate Tensile Stress and Young's modulus increase with increasing surface Ni percentage in Cu-cored NWs. However, in Ni-cored NWs these values decrease with the increase of surface Cu percentage. Also, for the same surface percentage of Ni in Cu-cored NW, the values are higher in linearly graded FGMs than that in exponentially graded FGMs. While in Ni-cored NWs, exponentially graded FGM shows higher values of UTS and E than those in linearly graded FGM. Thus, grading functions and surface percentages can be used as parameters for modulating the mechanical properties of FGM nanowires.