The three men have repeatedly said they would not seek clemency because such a request has to be accompanied by an admission of wrongdoing.
The three men - Amrozi, Ali Gufron and Imam Samudra - were sentenced to death in autumn 2003 for their part in the bombings, which killed 202 people, most of them Western tourists.
The men have said the attacks were in revenge for Muslim deaths in Afghanistan and elsewhere and that they were sanctioned under their interpretation of Islam.
Indonesia never reveals when executions are going to take place in advance, and there were no indications on Thursday that their deaths were imminent.
Mohammad Mahendradata, the men's lawyer, said he had yet to be informed of the court's decision.
He said he would attempt to challenge it further, but gave no more details.