The Pentagon says there are about 11,000 US troops currently deployed in Afghanistan - a significantly higher number than was previously disclosed.
Officials say the new tally includes temporary and covert units as well as regular forces.
It had previously said there were 8,400 troops in the country.
The announcement comes as the Pentagon prepares to deploy as many as 4,000 more troops to Afghanistan to help defeat the Taliban.
While the Pentagon said the move was a step in increasing transparency, it did not provide counts of US troops in Iraq and Syria.
"This is not an attempt to bring more forces in, but it is an attempt to actually clarify a very confusing set of reporting rules", said joint staff director Lieutenant General Kenneth McKenzie.
US Defence Secretary Jim Mattis has expressed frustration with the method of counting troops in conflict zones and said he would wait for a complete count in Afghanistan before making a decision on how many more to send.
The increase will be part of a new policy announced by President Trump last week.
Speaking to a crowd of US troops, he committed to stepping up the military's engagement in Afghanistan and said his approach would switch from nation-building to "killing terrorists".
The Taliban responded by saying that Afghanistan would become "another graveyard" for the US if it did not withdraw its troops.