Mr Kirimi is said to be the driver hired by the other three suspects to carry soil.
Mr Kirimi is said to have broken into the bank with others through an underground tunnel.
The other suspects are Mr Halford Munene Murakaru, 32, his brother Charles Mwangi Murakaru, 30, and friend, Julius Ndungu Wainaina.
A fourth suspect has been charged with breaking into a bank in Thika and stealing cash.
This comes after Mr Shem Karani Kirimi, 26, was arrested in Mtwapa on Friday in connection with the theft of over Sh50 million from the KCB Thika branch last month.
Mr Kirimi is said to have broken into the bank with others through an underground tunnel between November 18 and 20.
They allegedly stole Sh52,650,000, 95 Australian dollars, 185 Euros, 1,630 British pounds, 271,000 Tanzania shillings, 947,000 Uganda shillings, 5,781 US dollars, 40 South African rand and five Canadian dollars.
Mr Kirimi denied the charge before Thika Chief Magistrate Teresa Murigi.
His lawyer, Mr John Odera, pleaded that he be released on reasonable bond terms since there are others facing similar charges who were freed on bond.
Prosecutor Stellah Oyagi did not object to the application but requested the court to grant the accused similar bond terms as his co-accused.
She also requested the court to mention the case on December 14 for its consolidation with another suit in which three other suspects face similar charges.
The other suspects are Mr Halford Munene Murakaru, 32, his brother Charles Mwangi Murakaru, 30, and their friend, Julius Ndungu Wainaina, 30, who last week pleaded not guilty to two counts of stealing from the bank and handling stolen property.
They were released on a Sh4 million bond with two sureties each.
Ms Murigi ordered that Mr Kirimi be freed on a Sh4 million bond with two sureties of a similar amount and that he deposits his passport in court pending the hearing and determination of the matter.
Reports indicate that Mr Kirimi was the driver hired by the other three suspects to carry the soil dug from the tunnel for dumping in a thicket in Juja.