The effective ground thermal conductivity and borehole thermal resistance constitute information needed to design a ground-source heat pump (GSHP). In situ thermal response tests (TRTs) are considered reliable to obtain these parameters, but interpreting TRT data by a deterministic approach may result in significant uncertainties in the estimates. In light of the impact of the two parameters on GSHP applications, the quantification of uncertainties is necessary. For this purpose, in this study, we develop a stochastic method based on Bayesian inference to estimate the two parameters and associated uncertainties. Numerically generated noisy TRT data and reference sandbox TRT data were used to verify the proposed method. The posterior probability density functions obtained were used to extract the point estimates of the parameters and their credible intervals. Following its verification, the proposed method was applied to in situ TRT data, and the relationship between test time and estimation accuracy was examined. The minimum TRT time of 36 h recommended by ASHRAE produced an uncertainty of ~ ± 21% for effective thermal conductivity. However, the uncertainty of estimation decreased exponentially with increasing TRT time, and was ± 8.3% after a TRT time of 54 h, lower than the generally acceptable range of uncertainty of ± 10%. Based on the obtained results, a minimum TRT time of 50 h is suggested and that of 72 h is expected to produce sufficiently accurate estimates for most cases.