The cross was set up as a memorial for 19-year-old Anthony Devaney. The victim was fatally struck by a car while crossing Lake Street in May 2012.
The family put up the cross shortly after he died. It was removed once, then put back - but on Thursday, the cross was removed permanently.
Devaney's loved ones say the crosses are not religious symbols to them, but more of a reminder of the young man who died.
The victim's mother, Annmarie Devaney, said the removal of the cross brought back painful memories.
"It hurts. It's like reliving the moment again, it's like losing my son again pretty much," said Annmarie.
Shedding tears, Annmarie took the cross down to avoid any conflict with the city of Lake Elsinore, and with an atheist group that requested the cross be removed from public property.
"I don't understand why they need it to come up, but me being the mom and try to keep it positive, I want to do what's right and I don't want to make it a big deal or cause a scene," said Annmarie.
The American Humanist Association sent a letter to the city requesting the cross be removed. The group says it's unconstitutional, and a matter of separation of church and state. The family and the city then worked the matter out.
"We already planned a dedication of that memorial tree for March 22, and upon this request, we discussed with the family and they agreed to remove the memorial," said Lake Elsinore spokeswoman Nicole Dailey.
In a written statement to Eyewitness News, the American Humanist Association says it is "pleased with the city's decision to comply with the constitutional requirement of separation of church and state by removing the Latin cross from its property."
Minutes after the cross was removed, new crosses etched with "What happened to our freedom?," "R.I.P. 19 yr old Anthony," or "What if that was your child?" were put up in protest.