In March 1900, Shiba returned to Beijing as a military attaché, and was this present at the Japanese legation during the Boxer Rebellion. There his small force fought tenaciously and suffered almost 100% casualties over a 60 day period. He served with distinction during that campaign, aided by his prior knowledge of Beijing and by a large network of local spies. He protected the citizens and diplomats alongside several Western powers during the siege, and was subsequently awarded decorations by many of the western nations in the Eight-Nation Alliance. His name was also mentioned in "The Times".