The accused and relatives - who were barred from attending the hearing - broke into shouts of death to the government after the sentences were read, a reporter for the AFP news agency said.
Darfuri women at the court protested outside the courtroom but were escorted away by police.
The accused have one week to appeal before Omar Hassan al-Bashir, Sudan's president, signs the execution order.
Gibril Ibrahim, an adviser to the chairman of JEM, told al Jazeera: "The bloody regime that killed hundreds of thousands of people in cold blood in Darfur would not hesitate to sentence to death a few freedom fighters.
"But the court has no legal base and no constitutional base at all. Those people are prisoners of war and Sudan is party to the Geneva Conventions, hence it has no right to put these people into trial."
The UN has voiced concern that the courts do not meet international standards and urged the appeals court to review the sentences.
The attack on Khartoum in May was the first time an armed group had brought their fight to the capital.
The fighters were stopped at bridges over the Nile, a few kilometres from the presidential palace and army headquarters.