He was in the dock alongside Maurice Okere, a former Head of the County Treasury in Kidero's administration.
Kidero was hit with several graft related charges including bribery, money laundering and abuse of office.
He denied all the charges and was released on a Sh2million cash bail, execute a personal bond of Sh5 million and bond of Sh3 million with one surety of the same amount.
The former county boss was arrested on Wednesday by detectives from the Ethics and Anti-Corruption Commission (EACC).
Also accused are seven other individuals; among them top officials who served in Kidero's administration and two traders.
The officials stand accused of conspiring to commit corruption by authorising payment to a number of companies for services that were not rendered.
Their actions are said to have led to the loss of Sh213,327,300 in public funds between January 16, 2014 and January 25, 2016.
Kidero, in particular, allegedly received Sh24 million from Lodwar Wholesalers Ltd on diverse dates.
Chief Magistrate Douglas Ogoti further directed the Milimani Anti-Corruption Court registry not to receive charges after 8.30am.
With Kidero having been brought to court at 3pm, the judge noted that he "has noted the habit of prosecution bringing suspects to court late in the day".