In his resignation letter, he wrote "forces that do not support the [Make America Great Again] promise are - for now - ascendant within the White House", warning of the impact so-called "globalists" could have on Trump's agenda.
Gorka also was a member of the White House's Strategic Initiatives Group, which he described as a focal point for task forces collaborating with people outside government.
The memo, released by the White House, laid out in more detail a ban on transgender individuals serving in the U.S. armed forces that Mr Trump announced via Twitter last month, reversing a policy shift started under his predecessor, Barack Obama.More news: Taylor Swift Takes to Instagram to Announce New Single and Album
Gorka, who frequently appeared on cable news shows to tout Trump's policies, was seen to be a divisive figure within the administration by veteran intelligence professionals and diplomats as an ideologue with little real-world experience.
Bannon was removed from his permanent seat on the council in April, and several officials who came to the council under fired national security adviser Michael Flynn were also dismissed in recent weeks, including retired Col. Derek Harvey and the council's senior director of intelligence, Ezra Cohen-Watnick.
Sebastian Gorka, a fiery nationalist and Bannon ally, abruptly exits White House 2 down and 1 to go.
Gorka echoed comments Bannon made after he left the administration regarding the officials who now occupy the West Wing.More news: Ram Rahim Singh rape trial: CRPF, RAF to be deployed during hearing
During his stint in the White House, Gorka focused mostly on national security policy including rising fundamentalism in the Middle East and and combating China's economic warfare.
He criticized Trump's recent speech on Afghanistan, writing, "The fact that those who drafted and approved the speech removed any mention of Radical Islam or radical Islamic terrorism proves that a crucial element of your presidential campaign has been lost".
A person familiar with the situation said Kelly was coming up empty when it came to Gorka's role, though he recognized his efforts to promote Trump's message on television.More news: Lamborghini launches Alpha-One smartphone with Android Nougat