An email from Centers for Medicare and Medicaid Services administrator Marilyn Tavenner informed the staff of Cohen's plans to voluntarily resign at the end of the month and return home to California, The Hill reported.
Cohen, director of the Center for Consumer and Information and Insurance Oversight, had been on the job for two years.
His agency devised the regulations for the health care exchange but was not responsible for building HealthCare.gov, which failed after its launch in October, according to Bloomberg.
(Read more: New health law renewal extension coming)
Bloomberg noted that at a contentious hearing Oct. 30, Rep. Michael Burgess, R-Texas, demanded that Health Secretary Kathleen Sebelius fire Cohen, accusing him of misleading Congress about the website's problems. She refused, telling lawmakers she was responsible.
Bloomberg said Cohen didn't respond to an email asking about his plans.
Here are links to stories by The Hill and Bloomberg.