Another agent was wounded when they responded to a tripped ground sensor in the early hours of Tuesday morning.
Nicholas Ivie, 30, was the first agent killed since 2010, when a death led to a review of a botched US-run operation.
Operation Fast and Furious saw agents lose track of illegal guns from Arizona allowed into Mexico to target dealers.
Authorities said Agent Ivie, and another agent had been on foot near Naco, Arizona, about 5 miles (8km) north of the border, when gunshots rang out around 02:00 local time (08:00 GMT).
The second agent, who has not been identified, was airlifted to hospital and is being treated for non-life threatening injuries.
Speaking at a news briefing, authorities declined to say whether any weapons had been seized at the scene of the shooting.
"As they were walking up the trail, they reported taking gunfire," Cochise County Sheriff's spokeswoman Carol Capas told the Associated Press news agency.
"We have unknown suspect or suspects at this point."
Arizona's Republican Governor Jan Brewer, who has previously criticised the Obama administration's immigration policy, said in a statement: "Arizonans and Americans will grieve, and they should. But this ought not only be a day of tears.
"There should be anger, too. Righteous anger - at the kind of evil that causes sorrow this deep, and at the federal failure and political stalemate that has left our border unsecured and our border patrol in harm's way."
In December 2010 Agent Brian Terry was killed in a shootout with Mexican bandits. Later, his death was linked with Operation Fast and Furious, which was tracking illegal guns.
Two of the illegal weapons were found at the scene of the border agent's murder. Fast and Furious ended in early 2011.
No arrests were made in connection with Terry's death, but 14 officials were recently cited for possible disciplinary action in a US justice department investigation into the handling of the operation.
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