Football Kenya Federation (FKF) president Nick Mwendwa has been charged with four counts of fraud by the country's Directorate of Criminal Investigations (DCI).
The total amount of money Mwendwa and others, who were not in court, are accused of taking from FKF is just over Kshs 38 million - which is approximately $337,200.
Mwendwa was arraigned in court in Nairobi on Monday having spent the weekend in jail after his re-arrest on Friday.
He will spend another night behind bars, with a bail hearing set for Tuesday.
According to the police documents the offences took place between 4 March and 31 May this year.
Monday's court appearance comes two weeks after he was released on bail after a previous arrest.
Last Thursday the FKF announced the case against him was over as the court returned his Kshs 4 million (approximately $36,000) bail money.
However, the Kenyan police later clarified that it was not the fraud case which had been closed.
"It was only a miscellaneous application by police to have Mwendwa remanded in police custody for a longer period of 14 days to enable completion of investigation before being charged formally," Kenyan police spokesperson Bruno Shioso told BBC Sport Africa.
It meant that the DCI continued its investigations and eventually arrested him for a second time, with Mwendwa now being formally charged with corruption.