Manning in February admitted to leaking hundreds of thousands of classified documents to WikiLeaks. He has denied 12 charges against him, including aiding the enemy, but has to 10 lesser counts.
On Monday, Manning's defense lawyer, David E. Coombs, requested the judge drop the aiding the enemy charge, saying his client did not have "actual knowledge" that by leaking the documents to WikiLeaks, he was aiding the enemy, The New York Times reported.
However, the judge Thursday declined to drop the charge.
If Manning is found guilty of aiding the enemy, he could be sentenced to life in military custody with no chance of parole.