In the letter, Gorka accused Trump of caving into "forces that do not support the [make America great again] promise" that Trump made to his supporters during the 2016 campaign.
The White House, however, denied that Gorka had quit, but noted that he was no longer working for the administration.
Gorka's departure has revived discussion of a topic that had dogged him throughout his tenure: It was unclear what he actually did in the White House.
Gorka, a passionate defender of President Trump who regularly promoted the administration's agenda in media appearances, expressed disappointment in Trump's public statement announcing the deployment of 4,000 additional troops to Afghanistan―specifically, the failure to mention radical Islamic terrorism.
Sebastian Gorka gave his first interview on Saturday since "resigning" as Trump's deputy assistant, and despite the fact that neither he nor his mentor/Breitbart pal Steve Bannon are part of the administration anymore, the good doctor is confident they are now somehow even closer to the levers of power. A White House official, however, said Gorka did not resign but "no longer works at the White House".
'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.
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.
In an interview with the Economist published on Friday, Bannon said that Breitbart, which he has called a "platform for the alt-right", would never betray Trump, but would hold the president's feet to the fire if he deviates from his campaign promises.
The controversial figure's departure comes a week after chief strategist Steve Bannon left the White House.
Gorka, an ally of Bannon's who worked as a national security editor at Breitbart before joining the White House, reiterated during Saturday's show that he resigned over frustration with other factions of White House staffers.