Brayan Jimenez, 61, was placed under house arrest after posting a $1.5 million bond, $75,000 of it in cash.
Jimenez, who was detained in January in a disheveled and intoxicated state at an apartment in a posh suburb of Guatemala City, was extradited to the United States on Tuesday.
He is one of 39 officials and marketing executives accused by US prosecutors of soliciting and receiving tens of millions of dollars in bribes and kickbacks in a case that has sparked unprecedented crisis at FIFA.
Jimenez, an ex-member of FIFA's Committee for Fair Play and Social Responsibility, stood in the US federal court dressed in a white sweater and blue jeans to answer charges of corruption, money laundering, fraud and embezzlement.
His defense lawyer, Justine Harris, entered the plea "not guilty to all charges."
"Mister Jimenez is relieved to be reunited with his family," Harris told reporters after the hearing. "He is looking forward to facing the charges."
Implicated along with Jimenez is Guatemala football federation's secretary general, Hector Trujillo, who was arrested December 4 on a cruise ship in Florida.
Trujillo entered a not guilty plea December 30 and was released January 7 on a $4 million bond