In recent years, many disasters due to earthquakes and tsunamis occurred in various countries, including Japan. Two triple junctions exist below the Japanese archipelago and around Japan, where three plates meet to form a complicated crustal structure. To conduct research on the Tohoku earthquake, which accompanied the tsunami that devastated northern Japan in March 2011, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) constructed the scientific deep-sea drilling vessel Chikyu. To understand the mechanism of the earthquakes, a direct access to the fault zone is necessary. During drilling operations, the drill pipes are stressed by different forces and the occurrence of drill-string failures is high, which causes significant loss of money and time. This study focused on the definition of a practical fatigue assessment procedure useful to avoid failures during drilling operations. In this paper the proposed procedure is outlined, and the sensitivity analysis carried out to highlight most influencing parameters is presented.