Inadvertent human intrusion into a geological repository for radioactive waste is an incident of low frequency but high consequence. Until now, many studies have considered the frequency of deep borehole drilling for resource explorations in the site of the repository as a time-independent variable. However, future activities and technology of the human race will not be the same as today. Therefore, this study develops a new Markov chain model to estimate the frequency of human intrusion using time-dependent drilling frequencies based on the statistics of oil and gas exploration worldwide. The results showed that the frequency of human intrusion during the early time period is substantially reduced. After a few hundred years, the frequency steadily increases and approaches the value of the time-independent model. The low frequency during the early time period is attributed to enforcement of regulation, continuous knowledge of repository, and low utility of repository area. As these effects disappear, the frequency rapidly increases due to the future demand of resource exploration, which is a significant factor in increasing the risk of human intrusion. In addition, the reduction of average radio-toxicity in final waste is effective in reducing the risk, while the reduction of waste volume is insignificant for the frequency of human intrusion in the long-term.