The Senate has voted to approve Admiral Lisa Franchetti to lead the US Navy.
As Chief of Naval Operations she becomes the first woman to join the elite group of senior military officers who make up the Joint Chiefs of Staff.
Her nomination was approved 95-1, as the Senate pushed to fill critical openings in military leadership.
One Republican senator has been trying to block military appointments in protest of the Pentagon's abortion policy.
The 38-year Naval veteran is the former head of the US 6th Fleet and US naval forces in South Korea, and has also served as an aircraft carrier strike commander.
Her nomination by President Joe Biden marked the first time a woman has been put forward to head a Pentagon military service branch.
The US Coast Guard is led by a woman - Admiral Linda Fagan - but that branch falls under the Department of Homeland Security rather than the Department of Defense.
Senators also filled two other top spots.
General David Allvin was made chief of staff of the US Air Force and Lt Gen Chris Mahoney was approved as Assistant Commandant of the Marine Corps, a confirmation made more urgent after the Marine Corps Commandant suffered an apparent heart attack on Sunday, according to US media.
For the past nine months Alabama Republican Senator Tommy Tuberville has been blocking the Democrat-majority Senate from confirming nearly 400 military promotions over a Pentagon policy that pays the travel expenses of service members who have to go out of state to have an abortion.
On Wednesday night his Republican colleagues broke with him for the first time and dramatically read out the names of 61 nominees to allow each to get an individual floor vote, effectively bypassing his hold.
Alaska Republican Dan Sullivan chastised Mr Tuberville, saying that US troops' "careers are being punished over a policy dispute they had nothing to do with and no power to resolve".
Military officials and lawmakers alike have said he is putting US national security at risk during the conflicts in Ukraine and the Middle East.
"Both parties must work together to ensure that our military is fully staffed and fully equipped to defend the American people at any time, but particularly at this time of crisis," Senate Majority Leader Chuck Schumer said in a statement on Thursday.
Secretary of Defense Lloyd Austin said he is "glad" that some postings have been approved but added that the "unprecedented delay in confirming our military's top leaders has hurt our military's readiness and unnecessarily weighed down our military families".
"They are outstanding leaders who have faithfully served their country for decades, and I know they will continue to be great leaders of our force as they continue to tackle the crucial national security issues of these challenging times," he said in a statement.
"But we still have more than 370 superbly qualified leaders who have seen their nominations unnecessarily stalled."