And it was a hugely influential idea, that the trend towards liberal democracy is unstoppable, because it is, ultimately, what all people want, all over the world. It helped embolden the hawks in the Bush administration, making them feel the wind of historical inevitability at their backs when they went into Iraq three years ago.
But it is not what I said at all, Fukuyama insists. Hence his latest book, in which he tries to put the record straight. When I met him last week after he checked in at a fashionable hotel in Clerkenwell, London, for a tour to promote the book, he explained patiently: "The basic argument of The End of History was that people want to live in a modern society - not a democratic society necessarily. The desire to live in a political democracy is something that develops over time, particularly as societies get richer. I have never said you have this instant desire for democracy everywhere."
If he was misunderstood by the Iraq-war hawks then, he feels equally taken in vain by the anti-war movement today. Because he was a neoconservative who now rejects that label and who regards the Iraq invasion as a tragic mistake, the book has been greeted with glee in some quarters. He was one of the five "right-wing intellectuals" whose mugshots were paraded on the front page of The Independent earlier this month. Over the headline, "Are you listening, Mr President?" the newspaper said that the five had "demanded George Bush invade Iraq. Now they admit they got it wrong."
No, they don't. Fukuyama never advocated the invasion of Iraq. Yes, he was a neoconservative. For many opponents of the war, that makes him part of a right-wing plot to hijack American foreign policy, using 9/11 as a pretext for an imperial ambition.
"Everybody points to these letters that I signed, the Project for a New American Century, which is basically just Bill Kristol and a fax machine," he says. Kristol, as editor of the US conservative Weekly Standard, promoted what Fukuyama now regards as an excessively militaristic brand of neoconservatism.
"Part of the reason for writing the book is to rescue the reputation of neoconservatism," he says. In Europe, it is often regarded as an alien American doctrine. Yet Fukuyama cuts a surprisingly mid-Atlantic figure. Quietly spoken, given to extravagant understatement, he would not be out of place - apart from his Japanese ancestry - in any European university. He has an implausibly American lunch - a small shellfish platter and two black coffees. And at one point he fumbles in his wallet for a dollar bill in order to make a point about the Latin inscription on it that means "new order for a new age", which he says shows that the American belief in the inevitability of progress predated The End of History.
But his views on Iraq seem European in their worry about the counter-productive uses of US power. "I think that the United States needs to reconnect to the world. One of my biggest concerns is what's going to happen in terms of the backlash that the war is going to generate. That's what people ought to focus on."
A salient fact about the neoconservatives is that they were outsiders. Fukuyama's chapter on the neocon legacy ought to be compulsory reading for every Bush-hater, lucidly explaining how the movement arose among left-wing intellectuals at City College of New York. From working-class immigrant backgrounds, many were excluded from elite universities and many were Jewish. Fukuyama shares elements of that background.
His father's father emigrated from Japan to Los Angeles to avoid conscription in the 1905 Russo-Japanese war. His father was a liberal Democrat intellectual who settled in New York. Francis shared the neocon disillusion with the left and got a job as a policy wonk in the Reagan administration, working for his friend Paul Wolfowitz.
By the time of the Iraq war, Wolfowitz was deputy Secretary of Defence and arch hate figure of those who saw a neocon conspiracy. But it was through Wolfowitz that Fukuyama crystallised his opposition to the war. Fukuyama was commissioned in the summer of 2002 to produce a confidential study for the Pentagon of long-term strategy for the war on terrorism. But, by the time Fukuyama briefed Wolfowitz, in January 2003, and warned him that the invasion "was a very, very big risk" and that "they were rolling the dice" with the probabilities loaded against them, it was too late. The troops were already in the Persian Gulf and no one had time to focus on a strategy for nation-building to follow military "success".
At Johns Hopkins University in Washington DC, Fukuyama, 53, teachesinternational development. "People that have been around the development business tend to be fairly pessimistic about how easy it is for outsiders to influence the development of institutions or deal with corruption. One of my complaints about a lot of my neocon friends is that ... they seemed to think it was a matter of force and regime change and that institutions would take care of themselves."
So how does he react to the way he has been co-opted by the anti-war press? He laughs. "Well, you know, I think it's too bad, because I don't think you need further nails in the coffin of the first-term Bush doctrine." Which is why the new book is called After the Neocons, a word that he thinks is no longer useful.
"My purpose in writing the book is actually looking beyond the Bush administration. We are in for a tough patch. This should have been one of the lessons of Vietnam. It's fine to say we are going to use our military power, but if you use it imprudently, apart from generating all of this external opposition, you undercut the domestic basis for using it subsequently."
He despairs of American politicians. "As Iraq becomes seen as more and more of a failure," it will push the Republican base back towards isolationism, while Hillary Clinton's populist nationalism in opposing the takeover of US ports by an Arab company, he winces, is "terrible".
Fukuyama didn't vote for Hillary's husband, but thinks that President Clinton's foreign policy was right - to use force for humanitarian ends, but very reluctantly. "It's not a bad reality check for American foreign policy to say: if we can't get the majority of Nato members to go along with something, we probably shouldn't do it. That would have produced Bosnia, Kosovo, Afghanistan - but not Iraq."
He voted for Bush in 2000 but for John Kerry in 2004. His wife, Laura Holmgren, is an anti-war Republican too - rather more passionately anti-war than himself, he hints. (His three teenage children, he says, seem to regard his ideological battles with amused detachment.) But he was "happy in the end" that Bush was re-elected, "because I think Iraq would have deteriorated regardless."
And, he adds: "I think it's appropriate that Bush has to deal with the consequences of the intervention."
FROM THE NEW BOOK
* "The sudden end of Communism vindicated many of these [neocon] ideas and made them appear mainstream and obvious after 1989. This naturally did a great deal to bolster the self-confidence of those who had held them... [But] the fact that one was proven unexpectedly right under a surprising set of circumstances does not necessarily mean that one will be right the next time around."
* "In pushing for regime change in Iraq the Bush administration chose a high-risk, high-reward strategy. The risk the administration took was not absurd, especially in the light of what was believed about the WMD threat at the time. But it was premised on a very high, specific type of threat, and the administration rolled the dice in a way that required it to be correct simultaneously in several important calculations about future developments. Its self-confidence in its own judgement was misplaced since several of those calculations were questionable even at the time."
'After the Neocons' is published by Profile Books, £12.99
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