Endo began his career with Shonan Bellmare before moving on to Urawa Red Diamonds, where he won the AFC Champions League in 2017. In 2018 he was in Japan's squad for the World Cup but didn't feature in any matches. He then joined Belgian side St Truiden and after a season there was loaned to Stuttgart in 2019. He won promotion from Bundesliga 2 in 2019/20 and the deal was made permanent. Over the next three seasons Endo was a mainstay of the Stuttgart side, making 99 appearances. He was also a member of his country's World Cup squad in 2022 and appointed their captain the following summer.

Eyebrows were raised when Liverpool moved for 30-year-old Endo after losing out on both Romeo Lavia and Moises Caicedo to Chelsea. However, manager Jurgen Klopp said of the transfer: "He's a late bloomer, he was definitely underestimated, but he has improved every year since he has been in a proper football setting. When he came to Stuttgart he got an opportunity and never gave it away. When I saw him there's no chance I thought he was 30. On the pitch, he's a monster and wants to fight. He has been on my radar for a while. I'm personally really happy and now let's start working."

Endo took his time to settle initially and his first few games appeared to pass him by. As the season went on he became a pivotal part of Liverpool's midfield, breaking up opposition attacks and moving the ball forward. Keeping things simple, he was a vital part of Liverpool's midfield as the squad was decimated by injuries and his tenacity made him a firm crowd favourite. Endo didn't get as much game time in 2024/25, but showed the quiet authority that had already made him a respected figure at Anfield. He was no longer a fixture in every starting line-up, but his importance was obvious in the balance of Arne Slot’s midfield. When Liverpool needed control, particularly in matches that threatened to become frantic, Endo was the safety valve - closing down spaces, recycling possession, and calming the tempo. His ability to break up counter-attacks and shield the defence was central in several tight games that eventually tipped Liverpool’s way; a late tackle in one game against Wolves being treated like a goal. Though he rarely featured on the scoresheet, his worth came in those unseen contributions, the interceptions and disciplined positioning that allowed others to attack with freedom as Liverpool pushed towards a historic twentieth league title.