The case was identified at the Twentynine Palms Marine Corps Air Ground Combat Center and was confirmed by the U.S. Centers for Disease Control, the base said in a statement.
The base has 8,000 active-duty Marines and is the primary training center for Marines and sailors deploying to Iraq and Afghanistan.
The ill Marine is being treated as an outpatient at the base and will remain isolated at his barracks.
"He is doing well, and his condition continues to improve," the base statement said.
About 30 other Marines who had been "active socially" with him are being quarantined as well, the statement said. They will be permitted to return to full duty after five days if they display no flu-like symptoms, it added.
"The Marine Corps, along with all of the armed forces, is monitoring the health of our force to ensure we're taking the necessary precautions to educate and safeguard military and civilian personnel, as well as family members," the statement said.
At a Pentagon briefing earlier in the day, Marine Corps commandant General James Conway said the ill Marine at Twentynine Palms had not been to Mexico, where as many as 159 deaths have been attributed to the virus.