Kevin J. Counihan, right, CEO of HealthCare.gov George Ruhe | Washington Post | Getty Images

Meet HealthCare.gov's first-ever new boss—he's Connecticut Obamacare's old boss. The Obama administration on Tuesday moved to shake up the way the federal Obamacare health insurance exchange is run, appointing the head of Connecticut's successful exchange to lead HealthCare.gov. Kevin Counihan, who spent two years overseeing Access Health CT, becomes the first person whose sole responsibility is running HealthCare.gov, whose That federal marketplace sells private Obamacare insurance plans in 36 states, and closely deals with the 15 exchanges run by individual states and the District of Columbia. Counihan, who told reporters Tuesday that he was recruited for the federal job, also will be responsible for running the Center for Consumer Information and Insurance Oversight. Read MorePublic foots bills for firearm assaults

His appointment as CEO comes nearly 11 months after HealthCare.gov's botched launch, which was blamed in part on unclear lines of authority over the exchange. It also comes as HealthCare.gov prepares for Obamacare's second-enrollment season. Despite strongly recovering after its disastrous first two months well enough to enroll 8 million people by mid-April, HealthCare.gov is still undergoing work that could affect its operation when open-enrollment resumes Nov. 15. Counihan, during an interview with CNBC's "Street Signs," acknowledged that everything is not likely to work perfectly for HealthCare.gov this season. "There's going to be more problems . . . more work to be done, but every year it's going to be easier," said Counihan. He also said he said it is important to have "clear lines of accountability" in an organization like HealthCare.gov, which he added would benefit from some "private-sector principles." Counihan, 59, will report directly to Marilyn Tavenner, head of the federal Centers for Medicare and Medicaid Services, which is responsible for HealthCare.gov's operation. He previously served, from 2006 until 2011, as chief marketing officer for Massachusetts' health exchange, which was set up by then-Gov. Mitt Romney, and which became one of the templates for Obamacare.

Counihan's appointment comes after Access Health CT was singled out as having one of the best performances by any of the 14 individual states that sold health plans under the Affordable Care Act this year. The state said that since 2012 it has cut its uninsured rate among residents nearly in half—from 7.9 percent to 4 percent. That was largely due to Access Health CT, which in December 2013 became the first state in the nation to break its goal of private Obamacare enrollment, and which ended up with nearly double the enrollees originally projected. Access Health also largely avoided much of the issues that plagued HealthCare.gov and a number of state-run exchanges in the months after their October launch. Connecticut's exchange was seen as performing so well that Counihan earlier this year said it would be selling its exchange tech platform to other states that either wanted to scrap their own marketplaces or leave HealthCare.gov, which handles enrollment for 36 states.

Maryland, whose own state-run exchange was considered among the biggest Obamacare disasters, was the first state to move to adopt Connecticut's platform. Since then, eight other states have contacted Connecticut's exchange about using its technology, according to the US Department of Health and Human Services.

"I'm particularly pleased to welcome Kevin Counihan to the new Marketplace CEO role," said HHS Secretary Sylvia Burwell, who oversees CMS. "He brings additional operational and technological expertise to the position and will be a clear, single point of contact for streamlined decision-making. ... We are committed to instilling ongoing accountability for reaching milestones, measuring results and ensuring a successful open enrollment period." Counihan appeared Tuesday afternoon at a press conference in Hartford, where he was lauded by Connecticut Gov. Dannel Malloy and Lit. Gov. Nancy Wyman, who is the chairwoman of the state Obamacare exchange's board. Malloy, who has a sarcastic sense of humor, reportedly cracked that Counihan should have his head examined because of his decision to take the federal job. "It is an honor to be selected for this position and I look forward to the challenge ahead," said Counihan, who reportedly told reporters at that conference that "I did not seek the job out." "For the past two years, I've been fortunate to work with incredible people at Access Health CT. The success we've had here is due to the team we've put together and the guidance and direction we received from Lieutenant Governor Wyman, Governor Malloy and the Access Health board." "My sincere thanks to the entire team for their hard work and dedication. It has been an absolute pleasure to serve the people of Connecticut in this role." Wyman said that Counihan's departure is "a loss for the state, but I know he'll bring his strong commitment and considerable skill to his new role, and that is good for the nation." Connecticut has not yet decided on a replacement for Counihan. Read MoreGov't delivers Obamacare contraception compromise

Home page of Access Health CT Source: Access Health CT