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Born in 1537 to the Shimotsuma clan, senior retainers of Honganji. The Shimotsuma had served Honganji as head retainers since the Kamakura period and traditionally used the character "rai" in their names. Rairen became a close aide to Kennyo, 11th head of Honganji, at a young age, and was recognized for his military talent. When the Ishiyama War began in 1570, Rairen served as the effective supreme commander of Honganji forces for ten years against Oda Nobunaga. He placed the musket-skilled Saika-shu under his command, secured the Mori navy's sea supply lines, and coordinated with various Ikko-ikki uprisings — displaying outstanding military skill in both strategy and tactics. At the First Battle of Kizugawaguchi in 1576, his combined force with the Mori navy crushed the Oda navy and caused Nobunaga great distress. After the peace of 1580, he followed Kyonyo out of Ishiyama. He continued to serve as a senior retainer of Honganji supporting Kyonyo thereafter, and into the Edo period the Shimotsuma clan remained the leading administrator-priests (bokan) of Higashi Honganji. He died in 1626 at the remarkable age of 89 — one of the longest-lived of all Sengoku commanders, who witnessed the rise and fall of Nobunaga, Hideyoshi, and Ieyasu, all three unifiers of Japan.

Cool-headed and decisive. Though he held the unusual position of military strategist for a religious order, he combined the coordinating ability to marshal diverse forces — the Saika gunners, the Mori navy, Ikko-ikki bands across the country — with the tenacity to hold out against Nobunaga for ten years. Among non-daimyo, non-warrior-class commanders, he was unquestionably at the very top.

Rairen's exploits in the Ishiyama War proved that a religious order could stand on equal footing with the Sengoku daimyo. The Honganji army he commanded was not a mere peasant uprising but an organized military force, and his work cemented the Ikko sect's presence in Sengoku history. The Shimotsuma clan continued as bokan (administrator-priests) of Higashi Honganji throughout the Edo period and remains a family supporting Honganji administration to this day.