The University of Mississippi has stopped flying the state’s flag on its campus because it features the Confederate battle emblem.
Mississippi students had urged for the removal of the flag from campus because of its associations with slavery.
The university chancellor ordered the flag to be lowered and said it was being sent to the archives.
It has been the state’s flag since 1894, and residents opted to keep the flag during a 2001 state-wide vote.
The student body senate voted to request removal of the flag, then was joined by two other student groups in the call.
“The University of Mississippi community came to the realisation years ago that the Confederate battle flag did not represent many of our core values, such as civility and respect for others,” said chancellor Morris Stocks.
The murder of nine parishioners at a historical black church in Charleston, South Carolina, in June renewed a debate about the place of the flag in US culture.
The suspect, Dylann Roof, has appeared in many photos holding the flag.
A month after the tragedy, the flag was removed from South Carolina’s capitol grounds.
The Confederate battle flag became a potent symbol for the southern states fighting the Civil War as they sought to break away from the union.
It is seen by some as an icon of slavery and racism while others say the banner symbolises their heritage and history.