The director of M.I.T.’s prestigious Media Lab stepped down on Saturday after an outcry over his financial ties with the disgraced financier Jeffrey Epstein, whose contributions to the proudly contrarian lab roiled and divided its members.

“After giving the matter a great deal of thought over the past several days and weeks, I think that it is best that I resign as director of the media lab and as a professor and employee of the Institute, effective immediately,” the director, Joichi Ito, wrote in an email to the provost of the Massachusetts Institute of Technology, Martin A. Schmidt.

Mr. Ito acknowledged this past week taking $525,000 of Mr. Epstein’s money for the lab, as well as $1.2 million for his personal investment funds. He stepped down less than a day after an article in The New Yorker described the measures that officials at the lab took to conceal its relationship with Mr. Epstein, who killed himself in jail last month while facing federal sex trafficking charges.