They may have had a jinx in the penalty shootout with the latest being their Euro U-17 final defeat to Spain earlier this year, but the Steve Cooper team remained calm in front of a 53302 turnout as substitute Nya Kirby sealed the issue after their goalkeeper Curtis Anderson denied Hinata Kida.
This is their third quarterfinal and first since 2011.
England sorely missed their leading goal scorer Jadon Sancho, and the Young Lions, who had pumped in 11 goals in the group stage, failed to find the target to settle for a goal- less stalemate against an overly defensive Japan.
They followed it up with Callum Hudson-Odoi, Philip Foden and even goalkeeper Anderson finding the target.
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Japan's Yukihari Sugawara, Taisei Miyashiro and Toichi Kozuki scored but Kida's attempt was thwarted in a crucial breakthrough for England, who failed to find the target despite a flurry of attacks in the regulation time.
England sorely missed their star attacking midfielder Sancho and the team struggled to get their formation right with Callum Hudson-Odoi or Philip Foden pressed into his position, but without any fruitful result.
Japan were so defensive that their first corner came in the 63rd minute.
The match slowly picked up pace after both the teams looked tentative with their moves in the first 10 minutes.
In the absence of Sancho, who has been recalled by his club Borussia Dortmund, Foden occupied the attacking midfielder's position in the right-wing.
Foden initiated the moves but they failed to finish and survived a couple of Japanese onslaught late in the first- half.
In the fourth minute, Japan had the first attempt at the goal when Soichiro Kozuki's right footed shot from the left side of the box was blocked by Curtis Anderson.
The best attack of the first-half came in the 27th minute, when Foden put a through ball to Brewster whose thunder strike rattled the post.
The match picked up pace towards the half hour mark with Foden initiating moves from the right. England continued their goal search even as Rhian Brewster and Angel Gomes missed back-to-back chances.
In fact, the Cooper side went into the break under pressure with the Japanese attack stepping on the gas, though the Young Lions defence held on to thwart attempts from Soichiro Kozuki and Keito Nakamura.
With seven minutes remaining, Kirby had a fine attempt at goal, only to be blocked by Yuki Kobayashi.