Counihan's appointment follows the disastrous debut of the federal website last October, which many people inside and outside the Obama administration agreed resulted at least in part from a poor chain of command within HHS.
Counihan will oversee the federal exchange and help coordinate with the state-run exchanges, HHS Secretary Sylvia Mathews Burwell said in a statement Tuesday.
"He brings additional operational and technological expertise to the position and will be a clear, single point of contact for streamlined decision-making," she said.
Connecticut under Counihan had one of the more successful exchange rollouts this year. About 218,000 people enrolled in private health coverage through the state's website. HHS said nine states had contacted Connecticut about using its website's technical infrastructure for their own.
Burwell had announced in June that she would seek out a CEO to serve as the point person for all exchange operations in preparation for 2015 open enrollment.