A penalty from Harry Mallinder gave England an early lead but Scotland levelled the scores before the opening try from Roti Segun on the way to an 11-6 lead at half-time.
Sam Underhill, Thacker and Joe Marchant provided the second-half scores as England scored 17 unanswered points after the break.
Head coach John Fletcher said: “We were pleased to get the four tries but feel that there’s still a lot to work on. We made a few too many errors, but Scotland more than played their part.
“The bench added something when they came on, which was great, and we now focus on attention on playing Wales in a couple of weeks and performing well against them.”
Tigers prop Owen Hills was included among the England replacements.
15 George Perkins (Oaklands College, Saracens)
14 Kai Little (Hartpury College, Exeter Chiefs)
13 Lucas Slowik (Filton College, Bristol)
12 Harry Mallinder (Rugby School, Northampton Saints)
11 Rotimi Segun (Stowe School, Northampton Saints)
10 Joe Marchant (Peter Symonds, Harlequins)
9 Jack Maunder (Blundells School & Devon, Exeter Chiefs)
1 Lewis Boyce (Prince Henry's, Leeds Carnegie)
2 Jack Walker (Prince Henry's, Leeds Carnegie) (Captain)
3 Jack Stanley (Truro College, Exeter Chiefs)
4 Stanley South (Whitgift School, Harlequins)
5 George Nott (Kings School Chester, Sale Sharks)
6 Sam Smith (Old Swinford Hospital, Worcester Warriors)
7 Sam Underhill (Sir Thomas Rich’s School, Gloucester Rugby)
8 Will Safe (Hartpury College, Gloucester Rugby)
16 Ollie Adams (St Pauls Catholic College, London Irish)
17 Owen Hills (QEW, Leicester Tigers)
18 Jack Spencer (Hartpury, Gloucester Rugby)
19 Huw Taylor (Old Swinford Hospital, Worcester Warriors)
20 Callum Chick (Gosforth Academy, Newcastle Falcons)
21 Alexander Mitchell (Lymm HS, Sale Sharks)
22 Charlie Thacker (Leicester Grammar, Leicester Tigers)
23 Taylor Prell (Giggleswick School, Leeds)