The 48-foot cross became a memorial to Korean War veterans in the 1950s. It was erected in 1954 and was dedicated at an Easter Sunday ceremony describing the monument as a "gleaming white symbol of Christianity."
However, the memorial was challenged in 2006 when the ACLU, along with the Jewish War Veterans Association and several local residents, argued the cross violated the constitutional separation of church and state.
"We support the government paying tribute to those who served bravely in our country's armed forces," said Daniel Mach, director of the ACLU Program on Freedom of Religion and Belief. "But we should honor all of our heroes under one flag, not just one particular religious symbol."
In 2006, the federal government obtained the title to the cross and its surrounding property by eminent domain, and declared the cross to be a national war memorial.
The 9th U.S. Circuit Court of Appeals ruled in 2011 that the cross violated the constitutional separation of church and state.
After the Supreme Court declined review, the case went back to federal court in San Diego, where U.S. District Judge Larry Burns ruled on Thursday that "it's time for finality" in the case.
Burns said he believed the cross doesn't represent a government attempt to promote religion but acknowledged that the appellate court ruled differently.
Burns ordered the cross be removed within 90 days, but stayed the order until all possible appeals have been exhausted.
Supporters of the cross said they might again petition the U.S. Supreme Court to intervene.
The Associated Press and City News Service contributed to this report.