Two other defendants were sentenced to 10 years in jail, and a sixth -- a woman -- was given three years behind bars. But the panel ruled that Dilnozahon Nishanbaeva would not serve her prison term until 2014 to give her time to raise her young child.
Kyrgyzstan introduced a moratorium on executions in 1998.
State Prosecutor Ryskulbek Baktybaev told RFE/RL's Kyrgyz Service that he was satisfied with the issue of the trial.
"Anyone who does not spare other peoples' lives must be severely punished," Baktybaev said. "Today's trial is an illustration of that, I believe. Three of the defendants were sentenced to death. Investigators had collected plenty of evidence to prove their guilt before the trial."
Lawyers for the defendants said their clients would appeal the verdicts.
The six defendants are suspected of belonging to the banned Islamist Hizb ut-Tahrir and Islamic Movement of Uzbekistan groups.
They were all accused of raiding Kyrgyz and Tajik border posts on May 12. The attacks left several Kyrgyz and Tajik soldiers dead.
Kyrgyz authorities say they are looking for nine other individuals suspected of involvement in the same attacks.