His lawyer had been granted two weeks to appeal the decision.
In February, the chief prosecutor ordered the Ethics and Anti-Corruption Commission (EACC) to charge Central Bank Governor Njuguna Ndung'u in a case related to the award of a tender to install security software at the bank.
The governor has denied involvement in the case and lodged a High Court petition against the order. In documents submitted at the time, Ndung'u said he was not involved in the tender process and that the tender was awarded by an authorised body.
Ndung'u was in Paris attending an event in his official capacity at the time of the tender, the documents said.
High Court Judge George Odunga said in his ruling on Monday, “I am not satisfied the petitioner (Ndung'u's) fundamental rights have been infringed by the state over proposed charges.”
Following an appeal from Ndung'u's lawyer, Odunga gave the governor 14 days to file an appeal and within which time he would not face arrest.
Ndung'u, who became central bank governor in 2007, weathered a political storm in 2012 after parliament tried to oust him over currency turmoil in 2011 when the shilling weakened sharply and inflation soared.
His term runs until February 2015.