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We present an algorithm for the fast and accurate simulation of nanoscale devices. The idea underlying the algorithm is a divide-and-conquer method based on the nonequilibrium Green’s function formalism. This formalism has provided a unifying conceptual framework for the analysis of quantum transport in nanodevices and the computations therein are of significant interest across many areas of research. We offer two applications, the atomistic level simulation of silicon nanowires and the two-dimensional simulation of nanotransistors, which highlight the benefits of the divide-and-conquer framework. The inherently parallel algorithm presented here allows for computing resources to be flexibly allocated toward either solving problems of larger sizes in comparable time or speeding up the solution of a problem for a given size. Our algorithm facilitates the solution of problems orders of magnitude larger and, in most cases, was able to achieve substantial speedup, as compared to the current state of the art algorithm. Thus, the method presented here allows for large-scale simulation problems that can now be realized without the use of special purpose hardware or approximation methods.