"We found with the Caylee Anthony case how difficult it is to get a conviction in a U.S. court," McConnell said in an interview on "Fox News Sunday."
Republicans were angered by the Obama administration's decision last week to transfer accused Somali terrorist Ahmed Abdulkadir Warsame from a U.S. Navy ship, where had been held and interrogated, to the federal criminal system.
He's facing trial on a nine-count indictment, including allegations that he supplied material support to terror groups, including Al Qaeda in Yemen and the Somali group Shabab. Warsame is accused of trying to broker a weapons deal between the groups as well.
Republicans such as McConnell maintain that terror suspects such as Warsame need to be held in secure facilities outside the country such as the prison at Guantanamo Bay, Cuba, and tried by military commissions.
The minority leader's remarks were reminiscent of conservative criticism that erupted after a New York jury convicted former Guantanamo Bay detainee Ahmed Ghailani last year on a single count of conspiracy and acquitted him on more than 280 other counts.
(Ghailani still received a life sentence, and the administration's defenders argued that George W. Bush-era detention and interrogation policies weakened the Justice Department's case.)
The prospect of an outright acquittal by a jury has worried opponents of the Obama administration's intent to try as many terrorism suspects in U.S. courts as possible -- which seemingly led McConnell to invoke the Casey Anthony state-court murder trial in Florida. Anthony last week was found not guilty of killing her young daughter, Caylee.
"I don't think a foreigner is entitled to all the protections of the Bill of Rights," McConnell told Fox News. "They should not be in U.S. courts."