Abstract A method for calculating quality estimation of the magnetic field value measured by proton-precession magnetometers from data of single measurement is presented. This method is appropriate for frequency measurement algorithms which process time-series of signal’s zero crossing. Expressions for measurement error estimation are obtained taking into account signal decay and correlated noise. Presented formulas allow a result reliability to be estimated immediately in single measurement and give an opportunity for complex control of a device performance. Correlation and relaxation corrections are given. It was experimentally tested that the standard deviation of measurements is in a good qualitative agreement with presented error estimation.