E‐Defense, which is operated by the Japanese National Research Institute for Earth Science and Disaster Resilience, currently contains the world's largest 3‐dimensional shaking table (size: 20 × 15 m, maximum loading capacity: 12 000 kN). This facility has already implemented over 80 full‐scale or large‐scale experiments since its operation commenced in 2005. During these research activities, E‐Defense has encountered many challenges in the successful execution of various types of experiments within the designed experimental capacity and under the guidance of safe operational management. The experience gained in the past years using E‐Defense has led to the accumulation of knowledge on loading/shaking techniques, measurements for large‐scale specimens, table maintenance and operation, safety management, and specimen construction. This article highlights the major technical issues that have been encountered during the operation of E‐Defense and introduces the solutions that have been achieved. This is followed by brief summaries of some of the major experiments conducted since E‐Defense was commissioned.