Sir Jock Stirrup's comments come a week after Brigadier Mark Carleton-Smith, Britain's top military commander in the war-torn country, said the public should not expect a "decisive military victory" in Afghanistan.
Stirrup, the chief of the defence staff, told The Times that in both Iraq and Afghanistan, British troops were on a "journey that never finishes".
The 58-year-old air chief marshal said the mission in Afghanistan, where Britain has 7,800 troops fighting Taliban insurgents, was not a win or lose battle.
Britain's 4,100 troops in Iraq are likely to leave within a year, Stirrup said, with Iraqi forces "very close" to being able to handle the security situation alone.
However, Afghanistan would be a longer operation, he warned.
"Afghanistan is a very backward country... (militarily) it's going to be some years before we finish that project," he said.
Stirrup believes people should change their expectations of what can be achieved in Afghanistan.
"We should avoid the use of words like "win' and "lose' in the context of Afghanistan. It's not that sort of enterprise," he said.
"It's about helping the Afghans make progress in bringing their country towards the modern world. That's a very, very long journey where success is measured in each year looking a bit better than the one before."
Stirrup does not believe a military victory could be declared in Iraq either.
He said: "These things are more complicated... In both cases it's a journey. If you're talking about the development of a country, it's a journey that never finishes. There's no end point."
The aim of the mission in Afghanistan, as in Iraq, is to "help the government there extend governance to their people and to improve their lot.
"This is a very complex issue. It has to do with administrative capacity. It has to do with executive capacity, it has to do with the criminal justice system, with police and infrastructure.
"The armed forces are only there to create space within which political and other solutions can be delivered. They are a means to an end."
Asked if the war in Iraq has been successful, he replied: "We need to leave those judgments to historians."
Stirrup repeated his call for greater funding for Britain's armed forces, despite the credit crunch.
"The pre-requisite of a sound defence is a sound economy," he said.
"But you have to continue protecting your interests. You can't take a holiday from doing that."
He also said Princes William and Harry -- both army officers -- should be allowed to fight on the front line where possible.