Reproducibility has been well-studied in the field of food analysis; the relative standard deviation is said to follow the Horwitz curve with certain exceptions. However, little systematic research has been done on predicting repeatability or intermediate precision. We developed a regression method to estimate within-laboratory standard deviations using hierarchical Bayesian modeling and analyzing duplicate measurement data obtained from actual laboratory tests. The Hamiltonian Monte Carlo method was employed and implemented using R with Stan. The basic structure of the statistical model was assumed to be a chi-squared distribution, the fixed effect of the predictor was assumed to be a nonlinear function with a constant term and a concentration-dependent term, and the random effects were assumed to follow a lognormal distribution as a hierarchical prior. By analyzing over 300 instances, we obtained regression results that fit well with the assumed model, except for moisture, which was a method-defined analyte. The developed method applies to a wide variety of analytes measured using general principles, including spectroscopy, GC, and HPLC. Although the estimated precisions were within the HorRat(r) criteria, some cases using high-sensitivity detectors, such as mass spectrometers, showed standard deviations below that range. We propose utilizing the within-laboratory precision predicted by the model established in this study for internal quality control and measurement uncertainty estimation without considering the sample matrices. Performing statistical modeling on data from double analysis, which is conducted as a part of internal quality controls, will simplify the estimation of the precision that fits each analytical system in a laboratory.