Graphene, a two-dimensional (2D) material composed of carbon atoms arranged in a hexagonal lattice, has attracted tremendous attention due to its exceptional mechanical, electrical, and thermal properties. However, there is still a lack of consensus in the literature regarding the exact value of its thermal conductivity (κ). Both experimentally and computationally, there is a clear discrepancy in the literature, as some studies report ultrahigh (~5000 W/mK), while others find significantly lower κ (~100 W/mK) [1]. This could be a direct consequence of the fact that thermal transport in graphene is not accurately described by macroscopic diffusive laws; evidence of phonon ballistic and hydrodynamic transport has been theoretically predicted [2]. Significant scientific interest in tuning the thermal properties of 2D materials has been expressed lately via nanostructuration and chemical functionalization [3]. This of course requires a good understanding of the underlying mechanisms of thermal transport at the nanoscale and, for theoretical/computational studies, also an understanding of the effects of computational parameters and modeling limitations on the final calculated value. Here, we investigate computationally the effect of nanoperforation on the thermal conductivity of monolayer gra- phene through Nonequilibrium Molecular Dynamics. Towards this goal, we first examine and discuss the effects of the different computational artifacts on κ, ranging from the Boundary Conditions, the type of the thermostats, to more physical parameters such as the very definition of the thermal conductivity, the thermal gradient, the heat flux etc. After the study of the effects of the computational parameters, graphene samples with varying porosity levels were created by varying pore diameters, neck distances between pores, as well as pore size dispersion and spatial distribu- tion of the pores. The effective thermal conductivity of these samples is compared with that of pristine graphene. Our results show that even the least perturbation from the pristine configuration leads to a dramatic reduction of κ, con- sistent with previous experimental and computational studies. We also observe that the reduction in κ is more signif- icant for smaller neck distances, larger pore sizes and higher porosities. Overall, this study suggests that κ can be controlled by porosity engineering, while it also provides some deeper understanding of the mechanisms governing the effect of nanoarchitecturing on the thermal properties of graphene. These findings can offer significant insights into the impact of perforation on design and optimization strategies on graphene-based thermal management and en- ergy conversion devices