No, taxes will not be paid twice. Like other expert said, your 1099-R will have tax withheld reported (just like W2) that you will report on your tax return. But if taxes withheld were not enough then you might have to pay the difference. For example, your tax rate is 24% but tax withheld was only 20% then you have to pay that 4% difference. Company that holds IRA account do not know your total income so they will withheld certain amount but it might not be enough depending on your overall tax rate.
