The Liverpool midfielder, 33, suffered an ankle injury during a Premier League match against Sunderland in February that required surgery. He returned to the bench for Liverpool's final game of the season against Brentford, but his recovery was incomplete. He managed only half a match against Iceland on May 31 before being substituted due to discomfort.
At the time, Japan head coach Hajime Moriyasu had expressed cautious optimism.
"According to the medical reports, there is nothing to say he can't play. So we just believe, pray and wait."
Endo announced the decision on social media, writing in Japanese before providing an English translation of his message.
"As announced, I will be stepping away from the World Cup squad. Since my injury, I've done everything I possibly could up to this point, so I have no regrets whatsoever."
He addressed the emotional weight of the moment directly.
"Of course, there's frustration at not being able to participate in this World Cup, but more than that, I'm proud of how we've grown together since the Qatar World Cup — me as captain, leading this team and turning our goal of 'winning the World Cup' into something we can say as a matter of course."
Endo expressed confidence in the squad he leaves behind.
"The current team is truly a wonderful team. I believe they will overcome any adversity and show us sights we've never seen before."
He confirmed the retirement explicitly.
"With this campaign, I will be retiring from the national team. So from here on, I'll be cheering for the Japan national team as one of the fans."
His closing message carried the tone of a captain handing over a cause rather than simply departing it.
"The moment when the Japan national team wins the World Cup will surely come someday. Let's believe in that and cheer them on together. And let's unite Japan's strength as one so that moment comes in this tournament — everyone, let's take on the North and Central America World Cup together!! Everyone, give it everything you've got."
Endo will be replaced in the squad by Borussia Mönchengladbach forward Shuto Machino.
Only two days before announcing his retirement, Endo had spoken of Japan's ambitions in characteristically determined terms: "We will do our best with pride and passion to achieve something we've never seen before in Japan's soccer history."
That message now belongs to the players he leaves on the pitch. Japan face the Netherlands without their captain — and, for the first time since 2018, without Endo in their international setup at all.