Recently, nanoporous graphene has attracted great interest in the scientific community. It possesses nano-sized holes; thus, it has a highly accessible surface area for lithium adsorption for energy storage applications. Defective graphene has been extensively studied. However, the lithium adsorption mechanism of nanoporous graphene is not clearly understood yet. Here, we present theoretical investigations on the lithium-ion adsorption mechanism in nanoporous graphene. We perform ab initio electronic structure calculations based on density functional theory. Lithium adsorption in a graphene nanopore is studied and adsorption sites are determined. We also study different lithium-ion distributions in graphene nanopores to determine the best lithium–nanoporous graphene structures for lithium-ion batteries. We show that lithium ions can be adsorbed in a graphene nanopore, even in a single layer of graphene. It is also shown that adding more nanopores to multilayer nanoporous graphene can result in higher Li storage capacity for new-generation lithium-ion batteries.