Gen Shōji was born on 11 December 1992 in Hyogo. He developed through Fresca Kobe and Gamba Osaka's youth ranks before attending Yonago Kita High School in Tottori, where his coaches converted him from a forward into a centre-back — a positional change that defined his career. He signed with Kashima Antlers in 2011, where he became one of the J1 League's most aggressive, ball-playing centre-backs across nearly a decade of high performances.
With Kashima he won the J1 League title in 2016, the J.League Cup, the Emperor's Cup in 2016–17, the Super Cup in 2017, and the AFC Champions League in 2018 — the full set of Asian club honours. His performance in the 2018 FIFA World Cup round of 16 against Belgium, where Japan led 2–0 before being heartbreakingly knocked out, is one of the most-discussed defensive shifts in Japanese football history.
In January 2019 Shōji moved to Toulouse in France's Ligue 1 for a reported €3.5 million, then returned to Japan with Gamba Osaka in February 2020. After spells at Gamba and a return to Kashima in 2023, he joined Machida Zelvia in 2024. With Machida he has played a starring role in the club's first AFC Champions League Elite campaign in 2025–26 — 38 J1 League appearances and 12 ACL Elite matches in the 2025 season, scoring 3 league goals from defence.
Composed on the ball, dominant in the air and tactically intelligent, Shōji is one of Japan's most experienced centre-backs and a candidate to lead the next generation of defensive coaches in Japanese football after retirement.