Attorneys for Bradley Manning had asked the judge to dismiss all charges against the 25-year-old former intelligence analyst because he's been detained for two years and nine months.
Prosecutors said the delays were reasonable, given the complexity of the case and the volume of classified material involved.
Manning faces 22 charges, including aiding the enemy, which carries a maximum life sentence. His court-martial is scheduled to start in June.
Manning is accused of sending Iraq and Afghanistan battlefield reports, State Department diplomatic cables, other classified records and two battlefield video clips to WikiLeaks in 2009 and 2010 while working in Baghdad.
The Obama administration has said releasing the information threatened valuable military and diplomatic sources and strained America's relations with other governments.
Manning supporters consider him a whistleblowing hero whose actions exposed war crimes and helped trigger the Middle Eastern pro-democracy uprisings known as the Arab Spring in late 2010.
In an online chat with a confidant-turned-government informant, Manning said he leaked the material because he wanted "people to see the truth."
Under military rules, defendants must be arraigned no more than 120 days after they are charged, although exceptions can be granted for a variety of reasons, including the need to access classified material.
Manning was arrested in May 2010 and was detained for 635 days before his arraignment last February.
But the judge ruled that only 90 days of that time counted against the 120-day clock and that the rest of the delays were reasonable.
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