Toby Young said his position had "become a distraction" for the work of the Office for Students after his appointment to the watchdog's board sparked criticism in parliament.
Critics of the appointment have highlighted multiple derogatory comments made by Young on social media in the past about women, gay people, and the disabled.
Writing in The Spectator, Young said the "caricature" drawn of him over the past week was "unrecognisable", while acknowledging his earlier comments were wrong.
An online petition calling for his sacking gathered nearly 220,000 signatures before Young announced his resignation.
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MP Robert Halfon, chair of the parliamentary education committee, criticised Young's articles about the working class and "what he calls progressive eugenics".
"Now, I find this incredibly dark and very dangerous stuff," said the lawmaker from the ruling Conservative party, during a parliamentary debate on Monday.
Dawn Butler, shadow equalities minister, said she was "flabbergasted" by the appointment.
Foreign Secretary Boris Johnson had come to Young's defence last week, writing on Twitter: "Ridiculous outcry over Toby Young. He will bring independence, rigour and caustic wit. Ideal man for job."
Prime Minister Theresa May on Sunday said although she had not known of Young's history, he could stay in the post as long as he did not repeat such comments.
Shadow education minister Angela Rayner said the episode "has cast great doubt on the judgement of the PM (prime minister) who failed to sack him in the first place," tweeting on Tuesday.