Fannie will pay a dividend of $5.7 billion, while Freddie will send $4.5 billion to the government as the housing market continues healing from the effects of the 2008 financial crisis.
Fannie and Freddie were each taken over by the government in September 2008 when the economy was on the brink of collapse.
The firms received nearly $188 billion in taxpayer help to stay afloat.
All told, Fannie received $116.1 billion from taxpayers and has now paid $126.8 billion in dividends to the Treasury Department.
But those payments don't count as paying off the taxpayer loan.
Freddie will have repaid $86.3 billion once it makes the June payment, $15 billion more than the $71.3 billion it borrowed.
Fannie expects to remain profitable for the foreseeable future, although its annual net income is expected to be substantially lower than its 2013 levels.
Fannie’s revenue included $4.1 billion from settlement agreements relating to private-label mortgage-related securities.
Fannie and Freddie back about 90 percent of all new mortgages and have a portfolio worth about $5 trillion, nearly half of all loans.
Although the two companies don't make loans to borrowers, they buy them from lenders and guarantee them against default, which helps provide for more lending.
The Senate Banking Committee is working on bolstering support for a bipartisan plan that would eventually eliminate Fannie and Freddie, and shift more of the mortgage risk to the private sector.
A restart of a markup is likely to happen late next week.
Panel members are discussing some changes to the plan crafted by Sen. Tim JohnsonTim JohnsonCourt ruling could be game changer for Dems in Nevada Bank lobbyists counting down to Shelby’s exit Former GOP senator endorses Clinton after Orlando shooting MORE (D-S.D.), chairman of the Banking panel, and Sen. Mike CrapoMike CrapoLive coverage of Sessions confirmation hearing Senate rejects Paul's balanced budget Dems attack Trump SEC pick's ties to Wall Street MORE (R-Idaho), the panel's top Republican with the aim of sending it to the Senate floor with a sizable majority.