England did fall behind with under a minute on the clock though, the boot of Scottish fly half Ben Chalmers put the hosts 3-0 to the good, but England hit back with two quick-fire tries.
First Purdy made space for himself and touched down just wide of the posts before some smart backs play eventually freed up Kibirige who dived over for his first Under 20s try in the corner. Burns added the extras to make it 12-3 with eight played.
England's third try came from Tompkins who dotted down for his maiden Under 20s score to make it 19-3, but Scotland scored their first after 27 minutes - former England Under 18s hooker Sam James touching down in the corner to make it 19-8.
A Burns penalty just before the break put England 14 points to the good at half time, and Head Coach Nick Walshe's side came out in the second half all guns blazing.
After going through the phases, the ball eventually broke to Stephenson who showed good strength to go over for his second try in as many weeks after 48 minutes and Burns' conversion made it 29-8.
But Scotland hit straight back, quick hands and smart running freed up replacement Chris Dean who dived over for Scotland as Ben Cooper added the extras.
England then added two tries in quick succession - first a deft grubber from replacement No. 10 Sam Olver bounced kindly for Kibirige who touched down for his second before a rolling maul freed space for BMW Man of the Match Itoje who rumbled over. Olver converted both to make it 43-15.
There was still time for England to score their seventh - No. 8 Chisholm peeled off a maul near the Scottish try line to dive over and bring the game to a close.
"We're pleased to get the win - we knew it would be a tough game, and so it proved. Scotland fronted up but I'm pleased that we were able to perform well and score some nice tries.
"We've got a bit of time off now, so we'll look at the game and then regroup before we take on Ireland in Northampton - our first home game, and one we're really looking forward to."
Captain Callum Braley added:
"It was important for us to get a win tonight and get our Six Nations up and running. The lads were hurting a fair bit after last week's defeat against France, so we owed it to ourselves to go out and perform and thankfully we delivered with a good win tonight."
Points: Purdy 1T, Kibirige 2T, Tompkins 1T, Stephenson 1T, Itoje 1T, Chisholm 1T; Burns 3C, 1P, Olver 2C
England Under 20s starting XV against Scotland
15 Nathan Earle (Saracens)
14 Zach Kibirige (Newcastle Falcons)
13 Nick Tompkins (Saracens)
12 Tom Stephenson (Northampton Saints)
11 Henry Purdy (Leicester Tigers)
10 Billy Burns (Gloucester Rugby)
9 Callum Braley (Bristol Rugby, captain)
1 Danny Hobbs-Awoyemi (Northampton Saints)
2 Jack Walker (Leeds Carnegie)
3 Paul Hill (Leeds Carnegie)
4 Maro Itoje (Saracens)
5 Charlie Ewels (Bath Rugby)
6 Ross Moriarty (Gloucester Rugby)
7 Will Owen (Leicester Tigers)
8 James Chisholm (Harlequins)
16 Tom Woolstencroft (Bath Rugby) on for Jack Walker 63 mins
17 Alex Lundberg (London Wasps) on for Danny Hobbs-Awoyemi 46 mins
18 Harry Rudkin (Leicester Tigers) on for Paul Hill 70 mins
19 Tom Ellis (Bath Rugby) on for Ross Moriarty 49 mins
20 Joel Conlon (Exeter Chiefs) on for Joel Conlon 65 mins
21 Stuart Townsend (Exeter Chiefs) on for Callum Braley 65 mins
22 Sam Olver (Northampton Saints) on for Billy Burns 46 mins
23 Howard Packman (Northampton Saints) on for Tom Stephenson 48 mins
Content courtesy of RFU