On his first official visit to Japan since taking office in June, Lee met Ishiba at the premier's residence in Tokyo to discuss bilateral ties between the Asian neighbours, including closer security co-ordination with the United States under a trilateral pact signed by their predecessors.
"As the strategic environment surrounding both our countries grows increasingly severe, the importance of our relations, as well as trilateral co-operation with the United States, continues to grow," Ishiba said in a joint announcement with Lee after their meeting on Saturday.
The leaders agreed to resume shuttle diplomacy, expand exchanges such as working holiday programs, and step up co-operation in defence, economic security, artificial intelligence and other areas.
They also pledged closer co-ordination against North Korea's nuclear and missile threats.
The snap election victory of the liberal Lee - following the impeachment of conservative President Yoon Suk-yeol for declaring martial law - raised concerns in Tokyo that relations with Seoul could sour.
Lee has criticised past efforts to improve ties strained by lingering resentment over Japan's 1910-45 colonial rule of the Korean Peninsula.
The South Korean government last week expressed "deep disappointment and regret" after Japanese officials visited a shrine in Tokyo to Japan's war dead that many Koreans see as a symbol of Japan's wartime aggression.
In Tokyo, however, Lee reaffirmed support for closer relations with Japan as he did when he met Ishiba for the first time in June on the sidelines of a Group of Seven summit in Canada.
Despite their differences, the two US allies rely heavily on Washington to counter China's growing regional influence.
Together, they host about 80,000 US troops, dozens of American warships and hundreds of military aircraft.
We "agreed that unwavering cooperation between South Korea, the US and Japan is paramount in the rapidly changing international situation, and decided to create a virtuous cycle in which the development of South Korea-Japan relations leads to stronger co-operation", Lee said alongside Ishiba.
In Washington on Monday, Lee and Trump are expected to discuss security concerns including China, North Korea, and Seoul's financial contribution for US forces stationed in South Korea - something the US leader has repeatedly pressed it to increase.
