Although, he go on to admit the governing body may do things differently in the future after the Young Lions, considered as favourites for the title in Israel, became the first side to exit the competition after defeats to Italy and Norway put the semi-finals beyond them with a game to spare.
A key issue for Stuart Pearce's side was the string of high-profile players unavailable, with eligible players like Alex Oxlade-Chamberlain, Phil Jones and Danny Welbeck instead linking up with the senior side.
FA chairman Bernstein on Sunday defended the decision for such players to join up with Roy Hodgson's side for the friendlies against the Republic of Ireland and Brazil, but suggested the system will be looked at going forwards.
"I think when this sort of thing happens, we have this sort of disappointment, you've got to learn from it," Bernstein said.
"We do have to sit back and just review what we're doing strategically.
"We actually put a lot of focus on to this particular tournament. We regard it as being a very important development tournament for our players.
"It is disappointing but we will learn from it, and it may be that we organise things differently in the future, but that is going to be really for Club England and the FA to sit down and just review what we are doing and how we are doing it.
"You can only balance your resources and play them the best way you think is possible. Hindsight is a great thing in these sorts of situations.
"I think in this particular case, a development match in Brazil building up to a World Cup was very important and I would certainly defend what we did in having the strongest squad that Roy Hodgson could get in Rio de Janeiro."
Bernstein is in his last few weeks as FA chairman, with former BBC director general Greg Dyke succeeding him in July.
Under-21s boss Pearce could also soon be leaving the FA as his contract is up at the end of the month.
Young Lions captain Jordan Henderson wants the former left-back to be kept on, but Bernstein was coy on his future.
"That was something we always said would be decided after this tournament and that hasn't changed," said Bernstein, speaking at a 'Football For All' aimed at eliminating racism and violence from the sport.
"We will be sitting down as a Club England team in the very near future, I suspect within the next couple of weeks, to make that decision.
"Overall I have been very impressed with him, absolutely.
"I think his record has been good, he has won an awful lot matches, qualified regularly for tournaments.
"This tournament has been disappointing but I don't think it should be taken totally out of context in terms of his long-term deliveries, because on the whole he has delivered very well."