The payment was reportedly made in December, and last week President Trump said in an interview that the kingdom had "already deposited $1 billion in the bank."
However, earlier in the week, the Pentagon could not confirm to the network whether or not the payments had taken place.
"Consistent with the President's guidance to increase partner burden-sharing, the Department of Defense has engaged Saudi Arabia on sharing the cost of these deployments, which support regional security and dissuade hostility and aggression," Pentagon spokeswoman Cmdr. Rebecca Rebarich said.
Rebarich said that Saudi Arabia had "made the first contribution," but that "discussions are ongoing to formalize a mechanism for future contributions that offset the cost of these deployments."
The deployment of additional US troops started in September after attacks on Saudi oil facilities.
The funds will reportedly cover the US's overall cost of deploying troops, including fighter jets and Patriot missile defense batteries meant to protect Saudi oil fields from further attacks from Iran.
"While we will not comment on specific bilateral defense agreements, more broadly the United States encourages burden-sharing among partners in support of shared security interests, to include defense of the (Persian) Gulf," a State Department official told CNN.