A rapid source fault estimation and quantitative assessment of the uncertainty of the estimated model can elucidate the occurrence mechanism of earthquakes and inform disaster damage mitigation. The Bayesian statistical method that addresses the posterior distribution of unknowns is significant for uncertainty assessment. Particularly, the Metropolis-Hastings (M-H) method, a kind of the Markov chain Monte Carlo (MCMC) method, generally has many applications, including cosesimic fault estimation. However, this method exhibits a trade-off between the transition distance and the acceptance ratio of parameter transition candidates and requires a long mixing time, particularly in solving high-dimensional problems. This necessitates a more efficient Bayesian method. In this study, we developed a fault estimation algorithm using the Hamiltonian Monte Carlo (HMC) method, which is generally considered to be more efficient than the other MCMC method but not sufficiently feasible, to estimate the coseismic fault for the first time. HMC can conduct sampling more intelligently with the gradient information of the posterior distribution. We applied our algorithm to the 2016 Kumamoto earthquake (Mj 7.3), and its sampling converged in \(2\times {10}^{4}\) chains, including \(1\times {10}^{3}\) burn-in chains. The estimated models satisfactorily accounted for the input data; the variance reduction was approximately 88 %, and th estimated fault parameters and event magnitude were consistent with those reported in previous studies. HMC could acquire similar results using only 2 % of the -H chains. Moreover, the power spectral density (PSD) of each model parameter's Markov chain showed that this method exhibited a low correlation with the subsequent sample and a long transition distance per step. These results indicate that HMC has advantages in terms of chain length than M-H, expecting a more efficient estimation for a high-dimensional problem that requires a long mixing time or a problem using non-linear Green's function, which has a large computational cost.