He served as Speaker of the House of Representatives from November 2003 until August 2009, when the LDP lost its majority in the 2009 election.

Kōno served as speaker for the longest length since the set up of House of Representatives in 1890.

As he is one of the pro-China faction of the LDP, he came under pressure domestically in the spring of 2005 when anti-Japanese movements in China became intense due to then Prime Minister Junichiro Koizumi visited the Yasukuni Shrine which he opposed the visit to.

During his tenure as Chief Cabinet Secretary, in a speech titled the official statement he made in 1993, made after historian Yoshiaki Yoshimi announced he had discovered in the Defense Agency library in Tokyo documentary evidence that the Imperial Japanese Army established and ran comfort stations, he admitted that the Japanese Imperial Army had been involved, directly and indirectly, in the establishment of comfort stations, and that coercion had been used in the recruitment and retention of the women.

His subsequent call for historical research and education aimed at remembering the issue became the basis for addressing the subject of forced prostitution in school history textbooks.