It's been a long journey for the embattled Fannie Mae. Years of heavy losses are now reversing and the company expects many quarters of profit in the future.

Things are so good at Fannie Mae, that it is putting aside money to begin paying federal income tax again.

It will be the first time the government-sponsored enterprise will start paying taxes since going under conservatorship, with the Federal Housing Finance Agency acting as conservator, since September 2008.

In a conference call this morning, CEO Timothy Mayopoulos mentioned the $2 billion set aside in the second quarter to go towards the yearly tax bill. Fannie Mae is reducing its retained portfolio under FHFA stewardship and its deferred tax assets created a net-loss position that exempted the GSE from payments to the Internal Revenue Service.

Now that the company is in a period of profitability, once it expects for the long term, Fannie Mae is accruing cash each quarter for income tax.

One reason Fannie is making more money is the continued rises in the guarantee fees charged for securitizing mortgages.  For the first half of 2013, Fannie earned nearly $5 billion in g-fees, compared to less than $4 billion in the first half of 2012.

The g-fee for newly acquired mortgages is currently an average of 56.9 basis points. This compares to the average 40.3 g-fee charge in the second quarter of 2012. The indication is that the fee will continue to rise.

"We believe we are charging an appropriate amount to underwrite these loans," said Mayopoulos in reference to the rising cost.