McKinnon, who hacked into the systems from his home in London, said he was only searching the internet for information about aliens.
Speaking to Al Jazeera, Bob Ayers, a security expert and former US intelligence officer, said that the US wanted to "make an example" of McKinnon.
Ayers said: "He [McKinnon] has broken into some very sensitive computer systems and the US want to make an example of the young man.
"This has been done before in the US, there were two British people back in the early 1990s that broke into US systems and then they were allowed to be tried in the UK.
"One of them was fined $2,000 and the other wasn't even tried at all because the cost of the trial would have been too much according to the Crown Prosecution Service."
Judge Stanley Burnton said in his ruling that extradition was "a lawful and proportionate response to his offending".
"[McKinnon] believed in his words that '9/11 was an inside job', and that undoubtedly infuriated the Americans"
Alan Fisher, Al Jazeera's London correspondent
But McKinnon's lawyer Karen Todner called the ruling "hugely disappointing" and urged Alan Johnson, the home secretary, to intervene.
McKinnon, who has fought a three-year battle to avoid extradition, now has 28 days to decide whether to appeal against the ruling.
Janis Sharp, his mother, said she was "heartbroken" over the court's decision.
"If the law says it's fair to destroy someone's life in this way, then it's a bad law," she said outside the court.
Alan Fisher, Al Jazeera's correspondent in London, said there was "a possibility that we might see a further appeal to Britain's new supreme court".
He said McKinnon set up a series of computers to look into Nasa and US military computers so he could "essentially scan around 60 computers within about nine minutes".
"In a lot of the cases he left simple messages saying 'your security is rubbish'.
"But on at least one occassion he left a message saying that he believed that what was happening as far as the US foreign policy was concerned was state sponsored terrorism, and he believed in his words that '9/11 was an inside job', and that undoubtedly infuriated the Americans."
"This is from the Bush era, it is hold-over from the Bush era," she said, adding that Barack Obama, the US president, "would not want this to happen".
His lawyers has argued McKinnon could commit suicide or suffer psychosis if extradited, because of his mental health condition.
They say he could easily be prosecuted in Britain, where he would face a less severe sentence.
But the Crown Prosecution Service (CPS) ruled in February that the case was best brought in the United States.
McKinnon was arrested in 2002, after US prosecutors charged him with illegally accessing computers.