The White House confirmed the call on Tuesday.
Flake is one of four Republican senators who has been working with four Senate Democrats to craft a bipartisan immigration reform bill. In January the bipartisan group released a set of guidelines for passing immigration reform.
In February, Obama called members of the group to discuss their progress in passing an immigration reform bill. Obama was not able to reach Flake when he made the calls.
Obama also called Sen. Mark Kirk (R-Ill.) on Monday to discuss passing new legislation to reduce gun violence.