|Abstract : ||X-ray timing is a key tool for the study of compact objects and binary systems. The past few decades have seen significant development in period estimation tools and methods for analysing high energy pulsars. However, the commonly used methods in high energy astrophysics do not offer any means of easily and reliably estimating the uncertainties in the calculated parameters like the period or phase. Error estimation is important for assigning confidence intervals to the models we study but, due to their high computational cost, errors in the pulsar period were largely ignored. Some of the semi-analytical techniques used in the literature lack rigorous mathematical explanations. We present early results from numerical and analytical study of error distribution of extracted parameters of high energy pulsar data using the $Z_n^2$ method. For the first time we provide a formalism to reliably estimate the measurement uncertainties in pulsar periods, and validate the method with extensive testing and simulations. We show that where common heuristic methods can give error estimates that are wrong by more than an order of magnitude, our method provides reliable uncertainty values that agree with real as well as simulated data sets.