Needing a final day victory to ensure survival, the Bees were sunk by two second half goals from Roy O'Donovan and Luke Guttridge as the Cobblers head into Thursday night's play-off showdown with Cheltenham in fine fettle.
"That was us last year fighting relegation," Boothroyd said. "It was very stressful for us but this time we've finished a good few points better off.
"I think we've got what we have deserved this season. It's been a long season, we've had some brilliant performances and some rubbish performances, and Barnet away was one of those.
"We knew we would finish in the play-offs and I want to have everybody 100 per cent fit for the big games we've got coming up.
"It gives everybody an opportunity to stake a claim and to put themselves forward. I'll have lots of players available for training on Thursday night.
"We'll have more or less a full squad available and we need to make sure we make the most of that. I've got some really nice problems."