Bush won the popular vote the second time, in 2004, by 50.7 to Kerry's 48.3. He lost the popular vote the first time, in 2000, 47.87 to Gore's 48.38.
Ya know, I thought it was the first election when I read that at first. But just so that OP knows. . .
There have been 4 contested elections since the electoral college began:
In 1824: John Quincy Adams v Andrew Jackson--Four men in the same party ran for president. Jackson won the electoral and popular votes, but then the House of Representatives had to make a decision because the 4th person, Clay, threw all of his votes to Adams. This was the first election where popular vote count was kept and for good reason.
In 1876: Rutherford B Hayes v Samuel Tilden--Tilden had the popular vote, but lost to Hayes by one electoral vote.
In 1888: Benjamin Harrison v Grover Cleveland--Cleveland solidly won the popular vote, yet Harrison won the election. Harrison won this election because of Cleveland's high amount of popularity in the South where he was popular for wanting to reduce tarriffs to formerly Confederate states. Harrison won because he wanted to keep the tarriffs and areas with less populations threw all of their electoral college votes to Harrison. In the six southern states of Alabama, Georgia, Louisiana, Mississippi, South Carolina, and Texas, Cleveland received over 65% of the vote. The electoral college definitely did it's job here, because the purpose of the system is to keep one region from making the decision as to who becomes president.
In 2000: George W Bush v Al Gore--Had Al Gore been elected President, he would have become president purely by carrying less than half of the states. This was, yet again, the electoral college doing it's job by making certain larger states and more concentrated areas of the United States did not prevent representation from every area in the US.