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Victory will give the 22-year-old a place in the field for the Masters, US Open and The Open at St Andrews in 2027.
Whaley, who attends Florida State University, came into the contest as a major underdog against Leng Jr, who is 23rd in the world amateur golf rankings, some 67 places higher than the 22-year-old from Doncaster.
The on-course form looked to be following the rankings as Whaley slipped two down after the opening 18 holes in Sunday's 36-hole encounter.
However, Whaley fought back superbly, making back-to-back birdies on the second and third holes of his second round on his way to winning four holes consecutively.
With rain lashing down in Pennsylvania, both players took two of the next six holes before Leng Jr misread a putt on the 12th to hand his opponent a three-hole lead.
Whaley rounded off his win with a superb left-to-right putt for birdie at 15 to become the first English amateur to triumph in the US Amateur since Matt Fitzpatrick in 2013.
Prior to Fitzpatrick, Harold Hilton had been the last Englishman to won the title in 1911, with Scotland's Richie Ramsay (2006) the only other British winner since 1898.
Fitzpatrick went on to follow up his success at The Country Club in Brookline by winning the US Open on the same course in 2022.
Former US Amateur winners include Arnold Palmer, Jack Nicklaus, Tiger Woods, Bryson DeChambeau and Viktor Hovland.
Englishman WhaleyUS AmateurJack WhaleyEnglishmanUS Amateur ChampionshipAmerican Jay Leng JrMerion
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