Born in 1577 as the third son of Kennyo, the 11th head of Honganji. When his elder brother Kyonyo opposed the peace treaty ending the Ishiyama War and broke with their father, Kennyo disowned Kyonyo and designated Junnyo as successor. In 1592, at the age of 15, he became the 12th head of Honganji upon Kennyo's death. Backed by the protection of Toyotomi Hideyoshi, he stabilized the Honganji's position. During Sekigahara he leaned toward the Western army but was pardoned after apologizing to Tokugawa Ieyasu. However, when Ieyasu authorized Kyonyo to found Higashi Honganji in 1602, the Honganji was permanently split into eastern and western branches. Junnyo's lineage continued as "Nishi Honganji" (Hongwanji-ha, "Onishi-san"), which remains the largest Jodo Shinshu order to this day, centered on the Nishi Honganji temple at Horikawa-Shichijo in Kyoto with approximately 10,000 branch temples nationwide. Junnyo rebuilt the temple complex that had been burned in the wars, laying the foundations of the Nishi Honganji we know today.

In contrast to his hardline elder brother Kyonyo, Junnyo was moderate and cooperative by nature. As the successor chosen by his father, he carefully built relationships with the powers of the age, Hideyoshi and Ieyasu, working to preserve and develop the Honganji order. A religious leader who preferred building to destroying, preserving to fighting.

He preserved the Honganji order through the turmoil at the end of the Sengoku era and laid the foundations for today's Nishi Honganji (Jodo Shinshu Honganji-ha). The Nishi Honganji in Kyoto, home to the National Treasure Karamon gate and Goei-do hall, is registered as part of the UNESCO World Heritage Site "Historic Monuments of Ancient Kyoto." Thanks to Junnyo's steady stewardship, Nishi Honganji has remained the center of popular faith as Japan's largest Jodo Shinshu order for four centuries.