It was written in English and likely a young adult series. I believe it was a hardcover book and possibly from an Australian author, though I could easily be wrong. I have a feeling it was a series, but I'm not sure if I'm confusing it with other books from the author (see below). I believe it has been out for at least 10 years, probably longer, because I read it in middle school.
The book begins with a school boy seemingly hallucinating seeing a futuristic, armed girl. I think she might have been on the cover of the book, but again I could easily be wrong. The boy is later pulled into the space ship she is on (the school scenes were not real, I believe).
As I remember there was no real adults on the ship, although it might have been because they had all been killed off previously. I realise this seem similar to Earthsearch. Later in the book, or perhaps it was a later book in the series, other children joined the crew.
At the end of the book/series, it is revealed that Earth had been ecologically devastated (possibly by industrial pollution). The cloned (I think) children were on a return trip in space, so that by the time they get back to Earth, the planet is ready for human habitation again.
I recall reading in the afterwords that the author was writing some books set in the same universe, but about early space colonisation of the solar system. I think it was set before the above scheme to recolonise Earth was enacted. The author said we'll see "familiar names", presumably because the characters were later cloned for the recolonisation mission.
I read a couple of these "prequels" (or at least other books from the same author) but don't recall seeing such names. One of the books mentioned the Earth's oceans had turned toxic, though.