U.S. District Judge Larry Burns ordered the cross taken down within 90 days, the Los Angeles Times reported. But he then stayed his own order pending an expected appeal.
The cross has been converted into a war memorial by placing plaques honoring veterans at the site. But opponents, including Jewish veterans, say having a Christian religious symbol on public land violates the First Amendment.
"In spite of many secular changes to the memorial, its long sectarian history, as found by the 9th Circuit, effectively prevents the government from purging the religious connotation in any other way," Burns said in his opinion.
The legal wrangling has been going on for almost 20 years. The U.S. Supreme Court refused to hear the case in 2012 after an appellate court found the cross violates the First Amendment ban on an established church.
U.S. Rep. Duncan Hunter, R-Calif., who served in Iraq and Afghanistan, has been an outspoken supporter of allowing the cross to remain. A spokesman said Hunter expects the case to be back before the Supreme Court.