He said that the programme would not include the monitoring of private networks or internet traffic, as part of the US's commitment to "net neutrality" and following concerns from privacy advocates.
The new White House office of cyber security would report to the National Security Council and also the National Economic Council, Obama said.
But some critics say that the Obama administration's efforts are too poorly funded and that the czar would not hold enough authority to implement policies.
Also on Friday, the New York Times reported that the Pentagon planned to create a new military command for cyberspace aimed at conducting both "offensive and defensive computer warfare".
The programme, officials told the paper, would compliment the US government's efforts to combat cyber attacks.
The move to create a new role stems from a 60-day review of US cyber security ordered by Obama shortly after he entered office in January.
Plans to revamp the US government's approach to computer security also follow a series of attacks and security breaches on US networks, including reported breaches of the US electricity grid and the nation's F-35 fighter jet programme.
A US congressional panel also said in November that China had developed a sophisticated cyber warfare programme and stepped up its capacity to penetrate US computer networks to obtain sensitive information.
However, the issue of cyber security has been subject to tension between the US Department of Homeland Security and the highly secretive National Security Agency (NSA).
A senior homeland security official resigned in March after criticising the NSA for dominating efforts to combat cyber attacks and sidelining the Homeland Security department, AFP news agency reported.