"Today we have a new policy set by our new president. We have a new strategy, a new mission, and a new ambassador. I believe that new military leadership also is
McKiernan arrived in Afghanistan about a year ago and had been asking for extra troops as the Taliban campaign intensified.
New strategic plan
McChrystal is currently the director of the joint staff, a top military position. He comes from the warfare branch of the military rather than the conventional army, which marks a departure from previous appointments and recognises the complexity of the task in Afghanistan.
|Taliban fighters have taken control in parts
of Afghanistan [EPA]
He has led special operations forces, including "counter-insurgency", most prominently in Iraq from 2003 to 2008.
The replacement comes as top US officials, including General David Petraeus, who oversees military strategy for the region, implements Obama's new strategic plan for Afghanistan and Pakistan.
McKiernan played a crucial role in the current troop increase that is expected
to more than double the number of US soldiers in Afghanistan to 68,000 by the end of the year.
He had asked for an additional 10,000 troops in 2010, a proposal that appeared to meet resistance from Gates, who expressed reluctance to boost troops beyond the 68,000.
Al Jazeera's James Bays, who has reported regularly from Afghanistan, said McKiernan's replacement was a very important development.
"He commands all the American and Nato troops. He has been in effect fired from his job," he said.
"When McKiernan took up his job, he wanted more troops. He has been demanding them since. Now finally more troops are coming [but] he is not going to see the benefit of that.
"One source told me that the current thinking in the headquarters of the [Nato-led]International Security Assistance Force is that there is a problem between him and his new boss, General Petraeus - that he [Petraeus] sees him as perhaps a too conventional type of commander, and they wanted some fresh thinking."
Lieutenant General David Rodriguez, at present the head of US military forces in the eastern half of Afghanistan, has been lined up as McChrystal's deputy, a new position.
"These two officers will bring not just a renewal but a focus that we need in 2009," Michael Mullen, the chairman of the joint chiefs of staff, said.
Obama's plan for Afghanistan and Pakistan calls for a military push to reverse deteriorating security, and an increase in civilian aid and development assistance.
Hamid Karzai, the Afghan president, met Obama last week in Washington to discuss their joint approach to fighting the Taliban in Afghanistan and neighbouring Pakistan.
That meeting came amid claims that US air strikes in Farah province had killed at least 130 civilians.