The comments from the British historian, made during an interview with pro-Brexit commentator Darren Grimes, were widely condemned by politicians, publishers and universities.
The 75-year-old is an alumni of Fitzwiliam College at Cambridge and was made an Honorary Fellow in 2006.
The college said Mr Starkey's comments were "indefensible" and a statement on its website on Friday said the master of the college had accepted Mr Starkey's resignation.
"Fitzwilliam prides itself in leading the way in Cambridge in opening access to higher education for underrepresented groups," the statement says.
"Our student and academic bodies are diverse and welcoming to all. We do not tolerate racism.
"Although Dr Starkey holds no teaching role at Fitzwilliam, Honorary Fellows have the same responsibility as all members of our college to uphold our values."
Fellow historian and Cambridge professor Nicholas Guyatt had urged the university to “cut all ties” with Dr Starkey.
“Can’t speak for my employer but as someone who teaches history at Cambridge I'm ashamed of our connections with David Starkey and urge both the University and Fitzwilliam College to cut all ties with him,” he tweeted.
This story is being updated.