No over-age players in Japan Olympic men's football squad
Olympic men's football is an under-23 tournament, but up to three older players are allowed in each squad.
However, clubs do not have to release players as the Games take place outside the official FIFA international windows.
Japan team director Masakuni Yamamoto said it had been "difficult" to call up Europe-based players, even under-23s such as Real Sociedad attacker Takefusa Kubo.
Endo, 31, had been touted in Japanese media as a potential call-up along with Borussia Monchengladbach's Ko Itakura and Sporting Lisbon midfielder Hidemasa Morita.
Coach Go Oiwa said Japan were still aiming to win their first men's football medal since 1968.
"We're not going to the Paris Olympics for the experience," he said.
"We're going there as the Japan national team and we're going there to win a medal - the gold medal."
Japan have been drawn in Group D alongside Paraguay, Mali and Israel.
They qualified by winning the U23 Asian Cup in Qatar in May.
"I have chosen the best 18 players and four back-ups that were available to me," said Oiwa.