The accuracy in an X-ray pulsar-based navigation system depends mainly on the accuracy of the pulse phase estimation. In this paper, a novel method is proposed which combines an epoch folding process and a cross-correlation method with the idea of “averaging multiple measurements”. In this method, pulse phase is estimated multiple times on the sampled subsets of arriving photons' time tags, and a final estimation is obtained as the weighted average of these estimations. Two explanations as to how the proposed method can improve accuracy are provided: a Signal to Noise Ratio (SNR)-based explanation and an “error-difference trade-off” explanation. Numerical simulations show that the accuracy in pulse phase estimation can be improved with the proposed algorithm.