This paper proposes a methodology to define and quantify the precision uncertainties in aerothermodynamic cycle model comparisons. The total uncertainty depends on biases and random errors commonly found in such comparisons. These biases and random errors are classified and discussed based on observations found in the literature. The biases account for effects such as differences in model inputs, the configurations being simulated, and thermodynamic packages. Random errors consider the effects on the physics modeling and numerical methods used in cycle models. The methodology is applied to a comparison of two cycle models, designated as the model subject to comparison and reference model, respectively. The former is the so-called Aerothermodynamic Generic Cycle Model developed in-house at the Laboratory of Applied Research in Active Control, Avionics and AeroServoElasticity (LARCASE); the latter is an equivalent model programmed in the Numerical Propulsion System Simulation (NPSS). The proposed methodology is intended to quantify the bias and random errors effects on different cycle parameters of interest, such as thrust, specific fuel consumption, among others. Each bias and random errors are determined by deliberately preventing the effects from other biases and random errors. The methodology presented in this paper can be extended to other cycle model comparisons. Moreover, the uncertainty figures derived in this work are recommended to be used in other model comparisons when no better reference is available.