A simulation is presented here that serves the dual functions of generating a nanoporous membrane replica and executing the Brownian motion of nanoparticles through the virtual membrane. Specifically, the concentration profile of a dilute solution of fluorescent particles in a stochastic and SiO₂-coated carbon nanofiber (oxCNF), nanoporous membrane was simulated. The quality of the simulated profile was determined by comparing the results with experimental concentration profiles. The experimental concentration profiles were collected adjacent to the oxCNF membrane surface from time-lapse fluorescence microscopy images. The simulation proved ideal as an accurate predictor of particle diffusion—the simulated concentration profile merged with the experimental profiles at the inlet/exit surfaces of the oxCNF membrane. In particular, the oxCNF barrier was found to hinder the transport of 50 and 100 nm particles and transmembrane trajectories were indicative of anomalous subdiffusion; the diffusion coefficient was found to be a function of time and space.