Nairobi Anti-Corruption chief magistrate Eunice Nyuttu on Wednesday dropped the case against Nick Mwendwa after the Director of Public Prosecutions (DPP) again failed to produce any witnesses or evidence.
"I hereby discharge Mwendwa under section 87 (a) of the Criminal Procedure Code (CPC) for failure by the DPP to avail evidence before this court," Nyuttu said.
Mwendwa was arrested in November after the Kenyan government disbanded the Football Kenya Federation (FKF) and set up a caretaker committee to run football over alleged financial impropriety during his tenure.
He was charged with embezzling 38 million shillings ($337,000) received from the government and other sponsors as well as conspiracy to defraud the FKF of about $254,000.
Mwendwa, 43, had denied all the allegations against him.
Following the ousting of Mwendwa and the disbanding of the FKF, Kenya was suspended by football's world governing body FIFA in February over government interference in the running of the sport.
Kenya was excluded from the 2023 Africa Cup of Nations (AFCON) qualifiers which kicked off in June, and cannot host or play in any international matches under the FIFA ban.