The rebel known as Oliver Solarte controlled drugs and weapons smuggling operations in southern Colombia, President Juan Manuel Santos said.
He died in an attack on rebel positions near the border with Ecuador.
It is the latest in a series of blows to the guerrillas, who have lost many of their top leaders in recent years.
Farc setbacks
President Santos said the death of Oliver Solarte was an “important blow” to the left-wing group.
“”I want to tell them once again that if they keep doing what they are doing they will fall one by one, because we are not going to let down our guard and we have many others in our sights,” Mr Santos added at a news conference.
Hours earlier, the armed forces said it had killed six rebels in a separate operation in the region of La Macarena, further to the north.
Another 12 guerrillas surrendered in that operation, the army said.
The Farc is the oldest and largest of Colombia’s left-wing rebel groups.
In recent years it has suffered serious military setbacks, losing about half its fighters and many of its top commanders.
But it is still has several thousand guerrillas and operates in large areas of rural Colombia, particularly in the south and east, and is well funded by its involvement in the cocaine trade.
Source: BBC
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