Most known quantum magnetometers — proton, Overhauser, many types of sensors with optical pumping — have a periodic signal at the output. Its frequency is directly proportional to the magnitude of the magnetic field with high accuracy. Thus, by measuring this frequency, we can obtain the value of the magnetic field. In many applications, such as aeromagnetic measurements, we need to increase the sampling rate, but at the same time we reduce the accuracy of the measurements. The article aims to obtain the optimal frequency measurement algorithm depending on the characteristics of the equipment. We will also describe how to use a satellite navigation system as a time reference to ensure accuracy. All ideas are illustrated by experiments with various optically pumped cesium magnetometers. The reference standard frequency of the frequency counter used is 1 GHz. It is shown that for this frequency counter a sampling rate of up to 1 kHz can be obtained with any of the considered sensors.