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In this paper a signal model of the rubidium (Rb) atomic frequency standard is developed. The model combines an analysis of the atomic physics required to describe processes occurring within the Rb absorption cell with a feedback analysis of the clock’s servocontrol circuitry, and thus allows clock performance in terms of Allan variance to be predicted from a number of electronic and physical parameters. All previous models of the Rb clock have been limited to an analysis of the clock’s short‐term performance, Allan variance averaging times less than 10 000 s. However, by explicitly including the effects of discharge lamp intensity fluctuations, which are transformed into output frequency variations via the light shift effect, clock performance can be predicted for averaging times greater than 10 000 s. Furthermore, the present model is the first which incorporates the influence of an optically thick Rb vapor, along with the diffusion of optically pumped atoms to the walls of the absorption cell, into the calculation of clock performance. As part of the model’s validation, the calculations are compared with the results from a recent Rb clock long‐term performance experiment. Agreement between measured and predicted Allan variances for both short and long averaging time periods is excellent.