Psychometric properties of perceptual assessments, like reliability, depend on stochastic properties of psychophysical sampling procedures resulting in method variability, as well as inter- and intra-subject variability. Method variability is commonly minimized by optimizing sampling procedures through computer simulations. Inter-subject variability is inherent to the population of interest and cannot be influenced. Intra-subject variability introduced by confounds (e.g., inattention or lack of motivation) cannot be simply quantified from experimental data, as these data also include method variability. Therefore, this aspect is generally neglected when developing assessments. Yet, comparing method variability and intra-subject variability could give insights on whether effort should be invested in optimizing the sampling procedure, or in addressing potential confounds instead. We propose a new approach to estimate intra-subject variability of psychometric functions by combining computer simulations and behavioral data, and to account for it when simulating experiments. The approach was illustrated in a real-world scenario of proprioceptive difference threshold assessments. The behavioral study revealed a test-retest reliability of r = 0.212. Computer simulations without considering intra-subject variability predicted a reliability of r = 0.768, whereas the new approach including an intra-subject variability model lead to a realistic estimate of reliability (r = 0.207). Such a model also allows computing the theoretically maximally attainable reliability (r = 0.552) assuming an ideal sampling procedure. Comparing the reliability estimates when exclusively accounting for method variability versus intra-subject variability reveals that intra-subject variability should be reduced by addressing confounds and that only optimizing the sampling procedure may be insufficient to achieve a high reliability. This new approach allows computing the intra-subject variability with only two measurements per subject, and predicting the reliability for a larger number of subjects and retests based on simulations, without requiring additional experiments. Such a tool of predictive value is especially valuable for target populations where time is scarce, e.g., for assessments in clinical settings.