Harvard took the top spot on the list, knocking out Princeton, which placed first in the last three years, according to the U.S. News & World Report on Friday.
The third place was taken by Yale, to be followed by Massachusettes Institute of Technology (MIT) and Stanford. MIT and Stanford tied for the fourth slot.
California Institute of Technology (Caltech) tied for sixth with the University of Pennsylvania.
University of California in Los Angeles placed 25th on the list, while cross-town rival University of Southern California was 27th.
University of California in San Diego ranked 35th and University of California Irvine was 44th.
The rankings appear in U.S. News and World Report's "America's Best Colleges 2009" issue.
Rankings are based on factors such as student test scores, selectivity and graduate employment.