President Trump has expressed his gratitude for US Under Secretary of Defence John Rood's service on his post and wished him well.
The US Defence Department earlier stated that its top policy official was asked to leave his post.
In a separate statement, Pentagon spokesperson Alyssa Farah said Rood will resign at the end of February.
US Deputy Under Secretary of Defense for Policy James Anderson will fill the role until a permanent replacement is appointed and confirmed, Farah added.
CNN reported on Wednesday, citing two sources familiar with the matter, that Rood will leave his post soon after being asked for his resignation.
As the Pentagon's top policy official, Rood on 23 May last year certified to Congress that Ukraine had begun significant reforms and anti-corruption measures that would allow Washington to deliver $250 million in promised security assistance.
Rood's assessment at that time appeared to contradict the position of the White House, which has maintained that it temporarily blocked US aid to Ukraine over concerns about corruption.