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This paper investigates the use of pulsar-based navigation for deep-space CubeSats. A novel approach for dealing with the onboard computation of navigational solutions and timekeeping capabilities of a spacecraft in a deep-space cruise is shown, and the related implementation and numerical simulations are discussed. The pulsar’s signal detection, processing, and exploitation are simulated for navigation onboard a spacecraft, thus showing the feasibility of autonomous state estimation in deep space even for miniaturized satellites.