"Sebastian Gorka did not resign, but I can confirm he no longer works at the White House," a White House official said in a statement.
The official did not elaborate, but the statement suggested that Gorka had been fired.
Gorka had reportedly feuded with national security adviser General H R McMaster and was unhappy with the decision Trump announced this week - backed by McMaster and the U.S. military - to reorient US policy in Afghanistan.
Gorka, who frequently appeared on cable news shows to tout Trump's policies, was a divisive figure within the administration, seen by veteran intelligence professionals and diplomats as an ideologue with little real-world experience.
He is the latest in a string of hawkish or nationalist advisers to leave the National Security Council and other parts of the White House in recent weeks, suggesting that in the battle among Trump's foreign policy advisers, internationalist voices such as those of McMaster, Defense Secretary Jim Mattis and Secretary of State Rex Tillerson are prevailing.
Earlier, the conservative Federalist news outlet, citing multiple sources familiar with the situation, said Gorka, a counterterrorism expert, had quit. In a letter of resignation, Gorka expressed dissatisfaction with the current state of the Trump administration, the Federalist said.
"As a result, the best and most effective way I can support you, Mr President, is from outside the People's House," Gorka was quoted as saying in the letter.
Trump fired Bannon a week ago in the latest White House shake-up, removing a far-right architect of his 2016 election victory and a driving force behind his nationalist and anti-globalization agenda.
"Regrettably, outside of yourself, the individuals who most embodied and represented the policies that will 'Make America Great Again,' have been internally countered, systematically removed, or undermined in recent months. This was made patently obvious as I read the text of your speech on Afghanistan this week," he said in the letter.
A US citizen born in Britain with Hungarian parents, Gorka worked as national security editor at Bannon's Breitbart news website, where he often warned of Islamic terrorism.