Former Macclesfield midfielder Rooney, 21, who impressed Tykes manager Keith Hill during a week on trial at Oakwell, had recently been playing for Orlando City in the third tier of American football.
"We've hit a problem with the American FA, who can't yet give clearance," club director Don Rowing told Press Association Sport. "When you try and sign anyone outside of the transfer window the player has to be out of work for a period prior to the transfer window closing.
"Rooney had been playing in America and we were under the impression he had been out of work prior to August 31 when the window closes, but our application has come back showing an error.
"There seems to be some discrepancy between the date we thought he had been unemployed from and the date given by the American FA.
"The deal isn't dead, but if necessary we may have to sign him in January."