Tsutsui Junken served as a bushō during the Sengoku period. The Tsutsui clan were kokujin, or provincial landowners, in Yamato Province. In the Muromachi period, the Tsutsui served under the command of the Hatakeyama clan, but, owing to an internal conflict between Hatakeyama Yoshinari and Hatakeyama Masanaga, the kokujin under their command split-up, leading to chaos. In 1488, upon orders of Ashikaga Yoshihisa (the ninth shōgun of the Muromachi bakufu), Junken inherited the Tsutsui family after his father, Tsutsui Junson, died while en route to the capital of Kyōto. At this time, Junken was still immature so his uncle, Jōshinin Nobumori, served as his guardian.
In 1497, Hatakeyama Hisanobu rebelled against Hosokawa Masamoto and Hatakeyama Yoshitoyo and raised arms. Junken acted in concert and, together with Nobumori and Tōichi Tōharu, along with Ochi Iehide and Ochi Ienori (father and son) on the side of Yoshitoyo, attacked and ousted Furuichi Chōin from Furuichi Castle who at the time wielded influence over one-half of Yamato Province.
In 1499, Junken undertook the rites to enter the priesthood and adopted the name of Junken. In 1505, he reconciled differences with the Ochi clan and wed the daughter of Ochi Ienori. In 1506, he was attacked by Akazawa Tomotsune and Furuichi Chōin – bushō serving under Hosokawa Masamoto. In response, the kokujin of Yamato joined forces with the Yamato kokujin ikki (an alliance formed for the purpose of protecting the rights of landowners), rallying around the Tsutsui and Ochi clans to oppose Tomotsune and Chōin. Thereafter, these forces were repeatedly defeated by Tomotsune but, in 1507, after the assassination of Hosokawa Masamoto in an event known as the Eishō Disturbance, Tomotsune died in battle in Tango Province. This provided an opportunity for Junken and his allies to roll-back their losses, whereupon they ousted the Hosokawa army and returned to their original bases.
However, upon orders of Hosokawa Sumimoto (an adopted son of Masamoto), Azakawa Nagatsune (an adopted son of Tomotsune) deployed to Yamato. This led to the defeat and collapse of the kokujin ikki forces. In 1508, Ashikaga Yoshitane (the eighth shōgun) marched upon Kyōto with the backing of Ōuchi Yoshioki, the sengoku daimyō of Suō and Nagato provinces. The kokujin families broke-up again, with Junken and Tōichi Tōharu aligning with Ashikaga Yoshitane, Hosokawa Takakuni, and Hatakeyama Hisanobu, while Furuichi Chōin and Ochi Ienori joined the battle on the side of Ashikaga Yoshizumi, Hosokawa Sumimoto, and Hatakeyama Yoshihide.
Backed by Hatakeyama Hisanobu, Junken defeated Chōin and Nagatsune. After being cornered, Chōin killed himself while Nagatsune was captured and beheaded, enabling the revival of the Tsutsui clan. Conflicts with the Furuichi clan, however, continued thereafter.
In 1521, Junken’s younger brother, Junkō, acted on behalf of Junken and is surmised to have formally taken over the clan around this time. Junken lived a while longer but the details are uncertain.