When a frequency domain sensor is under the effect of an input stimulus, there is a frequency shift at its output. One of the most important advantages of such sensors is their converting a physical input parameter into time variations. In consequence, changes of an input stimulus can be quantified very precisely, provided that a proper frequency counter/meter is used. Unfortunately, it is well known in the time-frequency metrology that if a higher accuracy in measurements is needed, a longer time for measuring is required. The principle of rational approximations is a method to measure a signal frequency. One of its main properties is that the time required for measuring decreases when the order of an unknown frequency increases. In particular, this work shows a new measurement technique, which is devoted to measuring the frequency shifts that occur in frequency domain sensors. The presented research result is a modification of the principle of rational approximations. In this work a mathematical analysis is presented, and the theory of this new measurement method is analysed in detail. As a result, a new formalism for frequency measurement is proposed, which improves resolution and reduces the measurement time.