The paper focuses on scientific issues related to new application of pulsar signals for airplane-based navigation. A possible algorithm for processing of pulsar signals that consists of epoch-folding, matched filtering and detection is proposed and evaluated in this paper. The algorithm proposed is verified using the real experimental data obtained from the radio observatory Dwingeloo, the Netherland. The serious trouble in this study is that the total number of the input data within a repetition period is much more of the number of samples in a pulsar template taken from the EPN database. Therefore have been developed and evaluated two new algorithms for epoch-folding, which not only improve Signal-to-Noise Ratio of pulsar signals but as well reduce the number of samples of the output signals to the required number.