Stoke had knocked out 2017/18 winners Chelsea to reach the final for the first time but went behind to Samuel Edozie's deflected 39th-minute opener.
Man City then hit five goals in 15 second-half minutes.
Liam Delap netted a stunning solo goal before James Mcatee and captain Cole Palmer, pictured above lifting the Trophy, both struck braces.
Previous U18 PL Cup champions
2018/19: Manchester City