Founded in 1202 by Eisai under the patronage of the 2nd Shogun Yoriie as Kyoto's first Zen temple. Eisai traveled to Song China twice (1168, 1187), bringing back Rinzai Zen and tea seeds, becoming the father of both Japanese Zen and tea culture. At Kenninji he promoted tea cultivation alongside Zen practice. His 'Kissa Yojoki' is Japan's oldest treatise on tea. Kenninji is ranked 3rd of the Kyoto Five Mountains and houses Tawaraya Sotatsu's National Treasure 'Wind God and Thunder God' screens.

In 1259 (Shogen 1), the Chinese Chan master Lankei Doryu (Daikaku Zenji, 1213–1278) entered Kennin-ji and transformed it from a temple maintaining a tripartite arrangement of Tendai, Shingon, and Zen into a pure Rinzai Zen monastery. This reform, which completed what the founder Eisai had begun, played a decisive role in establishing Rinzai Zen as a specialist discipline in Kyoto. Lankei subsequently accepted the invitation of Hojo Tokiyori, fifth regent of the Kamakura shogunate, to become the founding abbot of Kencho-ji, and was posthumously granted the title Daikaku Zenji — the first Zen master title ever awarded by the Japanese imperial court.