Scot Gemmill’s side, who featured Hibs kid Ryan Porteous in central defence, led 1-0 at half-time thanks to a superb individual goal by Celtic winger Mikey Johnston.
Skipper Oliver Burke had earlier hit the post as Scotland created the better chances.
But England stepped up a gear in the second half and were level within four minutes as Everton winger Callum Connolly equalised from an Eddie Nketiah cross.
Five minutes later, Arsenal kid Nketiah sent a stunning strike from the edge of the box past Rangers goalkeeper Robby McCrorie to put England ahead.
With just over ten minutes remaining, Nketiah raced clear to beat McCrorie again and seal the win.
Scotland: McCrorie, Ralston, Taylor, Kerr, Porteous, Campbell, Gilmour, Wilson, Burke, Johnston, Hornby. Subs: Doohan, Harvie, Burt, Wright, Watt, Middleton, St Clair, Wighton, Hamilton.
England: Woodman, Kenny, Dasilva, Connolly, Clarke-Salter, Fry, Cook, Dowell, Vieira, Armstrong, Nketiah. Subs: Walker-Peters, Tomori, Davies, Abraham, Ramsdale, Konsa, Choudhury, Pearce, Nmecha.