Earlier this year Sgt Charles Martland was ordered to be discharged by Nov 1, and he has now been refused leave to appeal.
Martland, 33, was deployed to Kunduz Province where, in 2011, he and another soldier confronted and beat up a local commander accused of raping the Afghan boy.
He was reprimanded by a senior officer for a "flagrant departure from professionalism and even-tempered leadership" and discharged.
Duncan Hunter, a Republican congressman from California, said he had asked US defence secretary Ash Carter to review the case.
Mr Hunter said: "I hope that when making a decision between supporting an elite warrior like Martland, or a child rapist and criminal, the organisations or individuals in a position to make a decision will side with Martland."
The rejection of Martland's appeal by the US Army Human Resources Command came amid reports that US soldiers had been told to ignore abuse of children by Afghan allies.
The controversy centres around the practice called "bacha bazi" which means "dancing boys" and involves the sexual abuse of youngsters by powerful or wealthy men.
Vern Buchanan, another Republican congressman, said: "It is bad enough if the Pentagon is telling our soldiers to ignore this type of barbaric and savage behaviour but it's even worse if we are punishing those who try to stop it."
Pentagon and White House officials condemned reports that Afghan forces working with US soldiers had sexually assaulted boys.
They also denied the suggestion that US soldiers had been instructed to overlook human rights abuses.
White House spokesman Josh Earnest said: "The United States is deeply concerned about the safety and welfare of Afghan boys who may be exploited by members of the Afghan national security and defence forces.
"This form of sexual exploitation violates Afghan law and Afghanistan's international obligations. More broadly, protecting human rights, including by countering the exploitation of children, is a high priority for the US government."
In a report last year the US State Department said there were suggestions "security officials and those connected to the Afghan National Police raped children with impunity."