Very sketchy as I was about 8 the last time I watched it 24 years ago! A boy finds a way to get on a giant floating city which is nearly deserted and at the end I think it gets destroyed by a fleet of ships. That ends my brilliant clues.
I believe it is from the 80s, and was shown on the British TV channel ITV.
Sounds as though it might be Laputa: Castle in the Sky.
It was released in 1986, the city could only be reached by airship, and it was destroyed at the end, but not by the airships - it was destroyed so that its secrets could not fall into the wrong hands.
These are the two main characters, befriending the last of the city's guardian robots:
