The Young Lions created a number of chances and spent the majority of the second half on the front foot, but couldn't find an equaliser after finding themselves 2-0 down early in the second half.
Reiss Nelson pulled a goal back to give Cooper's side hope of salvaging a point, but they couldn't find their way past a resolute Swedish team.
England 1-2 Sweden
UEFA European U17 Championship
The Finals
Friday 6 May 2016
Baku, Azerbaijan
And the head coach believes his side paid the price for conceding two avoidable goals and a lack of ruthlessness at the other end.
'First and foremost we’ll always look at what we can do better. We’ve given two soft goals away tonight and they're mistakes at this level you can get punished for and unfortunately we've paid the price for it," said Cooper.
"It is part of learning though, and that is a key part of a young player's journey [through football], but of course on the night it's a difficult one to take.
"We've created a number of good chances ourselves and some of which go in on another day. Even when you've got those half chances, you've got to be looking to score so we know what we have to do better."
The Young Lions now have two days before their next game, and a chance to get some points on the board when they face France on Monday.
And with another two games to go in the group stage, Cooper knows his side's destiny is still in their own hands with a quarter final spot up for grabs for the top two nations in the group.
"We haven't said too much to the players at the moment, we won't get carried away too much whether it's a really good performance or bad performance," he explained.
"Everything that happens at this tournament will be a great education and a good part of their learning going forward.
"But we'll look at it in a bit more detail tomorrow, and the good thing about it is we've still got two more games to put some wrongs right and still make it a positive trip - we know we can still qualify.
"What I was really pleased with was the lads attitude and commitment to sticking to our game plan and playing in a style we want to see from our England teams.
"The group is still open and you can qualify in a number of ways, you can win or lose the first game and qualify, so it's still very much wide open and it will be interesting to see how it goes.
"We know what we have to do now and that's prepare for France on Monday."
