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Flow reactors are widely used to study the formation of various nanoparticles, such as carbon black, soot, nickel, titania, and silica. Such reactors provide well-controlled conditions, making them a favored laboratory tool to investigate the details of particle formation. Here we present NanoParticle Flow Reactor (NanoPFR), a detailed model to simulate nanoparticle synthesis in flow reactors. The model predicts the agglomerate fractal-like morphology and size distribution with a 2-variable sectional population balance model coupled with gas-phase chemistry. The particle formation processes employed in the code are tested using detailed discrete element modeling simulations and then used to predict carbon black formation from ethylene pyrolysis experiments from the literature. The code is a robust flow reactor predictive tool with a strong foundation that can serve as a basis for further development, including the simulation of other nanoparticles formation.