Having beaten Macedonia 2-1 in their opening clash in Prilep and drawn 1-1 at leaders Greece, the victory keeps England in second place - three points behind with a game in hand.
But possibly the biggest talking point after the full-time whistle was the fitness of Walcott - who had to be substituted at the interval.
The Arsenal forward only made his return from a lower back injury in last weekend's Premier League victory over Blackburn, but Pearce was adamant his latest scare was nothing to worry about.
"He got a dead leg when he bumped into Andy Carroll but he will be fine," he said.
"I can't see it lasting too long, I would have thought after the weekend he would okay.
"But obviously with his injury record early season, the physios thought it was prudent to bring him off the pitch.
"We've looked after him more than probably the injury entails."
Pearce revealed on Thursday that the 20-year-old could possibly be called into Fabio Capello's senior squad for Wednesday's World Cup qualifier against Belarus should the opportunity arise.
And he stated that may still be the case should he be needed.
"If they don't have any injuries in Ukraine tomorrow then I would have thought Fabio will go with the same squad," added Pearce.
"If they cop a few injuries then it will be situation to have a look at him, if Fabio so wishes.
"I know Theo and I know what he's like and the passion he's got to represent his country.
"If there's an opportunity there I'm sure he will do everything he could to be available."
Kieran Gibbs and Micah Richards put England into a commanding 2-0 lead before Muarem Muarem gave the visitors a lifeline just before the break.
And a whirlwind period shortly after the restart saw the scoreline read 3-3 within six second-half minutes, as Agim Ibraimi and Newcastle striker Carroll found the net before Gibbs put past his own keeper.
But a brace from West Ham debutant Zavon Hines and another from Carroll secured the points, and left Pearce with a host of differing emotions.
"It was a mixed bag to say the least," he said. "There's not too many 6-3 scorelines at Under-21 level for England that's for sure.
"There was some fantastic forward play, defensively we let in some poor goals but I think collectively, as a team, we probably have to defend a little bit better.
"But we know we've got talent in the squad to go and score a goal and create a goal and we demonstrated that tonight.
"Not only did we score six goals but we looked as though we could score one or two more as well.
"From my point of view, there's things to work on but things to work on in a positive manner as well."