The attack, carried out by a Saudi, was the worst act of terrorism in Kuwait's history.
Those charged include seven Kuwaitis, five Saudis, three Pakistanis, 13 stateless people known as bidoons, and another person at large, the prosecution said, cited by the official KUNA news agency.
Of them, 24 are detained in Kuwait and the remaining five will be tried in absentia. Among the latter are two Saudi brothers who allegedly transported the explosives to Kuwait. They are being held in Saudi Arabia.
Read: IS suicide bomber kills 25 at Kuwait Shia mosque
The prosecution charged two of the suspects with premeditated murder and attempted murder.
Two others were charged with training in the use of explosives, nine with assisting in committing the crime and the rest with knowing of the attack without informing the authorities.
An IS-affiliated group calling itself Najd Province claimed the bombing and also said it carried out suicide attacks at two Shiite mosques in Saudi Arabia in May.
IS considers Shias to be heretics and has targeted them across the region.
On Monday, the Kuwaiti cabinet decided to set up a permanent committee to "fight against all forms of terrorism... and extremism," and it will coordinate among various bodies in a bid to ensure security.
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