We obtained thermal desorption spectra of hydrogen for a small-size iron specimen to which strain was applied during charging with hydrogen atoms. In the spectra, a shoulder-shaped peak in the high-temperature side was enhanced compared with the spectra of the specimen to which only strain was applied. We also observed that the peak almost disappeared by aging processes at ≥ 373 K. Then, assuming that the shoulder-shaped peak results from hydrogen atoms released by vacancies, we simulated the thermal desorption spectra using a model incorporating the behavior of vacancies and vacancy clusters. The model considered up to vacancy cluster $${{V_9}}$$
V
9
, which is composed of nine vacancies, and employed the parameters based on atomistic calculations, including the H trapping energy of vacancies and vacancy clusters that we estimated using the molecular static calculation. As a result, we revealed that the model could, on the whole, reproduce the experimental spectra, except two characteristic differences, and also the dependence of the spectra on the aging temperature. By examining the cause of the differences, the possibilities that the diffusion of clusters of $${V_2}$$
V
2
and $${V_3}$$
V
3
is slower than the model and that vacancy clusters are generated by applying strain and H charging concurrently were indicated.