The agency said home prices rose 7.2 percent from the second quarter of 2012 to the same period of 2013, as prices rose for the eighth consecutive quarter.
In the final month of the second quarter, from May to June, prices rose 0.7 percent, consistent with the April to May increase.
The agency keeps track of prices of homes with mortgages backed by either the Federal National Mortgage Association or the Federal Home Loan Mortgage Corp., better known as Freddie Mac and Fannie Mae.
"The housing market experienced one of its strongest quarters since the boom in the middle of the last decade," said FHFA Principal Economist Andrew Leventis in a statement.
The agency said the seasonally adjusted Home Price Index rose in 47 states and the District of Columbia in the second quarter.
The top five in annual price gains were Nevada, California, Arizona, Oregon and the District of Columbia.