The first court hearing would be held in a Massachusetts District court on May 30, the judge ruled on Tuesday.
The 19-year-old Chechen-origin suspect is charged with conspiring to use "weapon of mass destruction", faces death penalty if convicted by the court.
He appeared alert, mentally competent, and lucid, the judge said.
Dzhokhar was arrested on Friday from a boat parked in the backyard of a house in a Boston neighbourhood ending days of massive manhunt to find the culprits of the Boston bombing attack.
He was admitted to a city hospital soon thereafter as he was badly injured with apparent gunshots wounds on head, neck, legs and hand.
Given the sensitivity of the case and his health condition, the authorities converted his hospital room into a court where District Judge Marianne B Bowler conducted the proceedings with Dzhokhar on his hospital bed and the two Assistant US Attorneys, William Weinreb and Indian American Aloke Chakravarty, representing the federal government.
While the indictment has been sealed, the Department of Justice in a press statement yesterday said the suspect has been charged on two counts of conspiring to use weapons of mass destruction and of malicious destruction of property by means of an explosive device resulting in death.
It also has a fine of $250,000.
"You have been charged with use of a weapon of mass destruction, in violation of and malicious destruction of property resulting in death," the judge told Dzhokhar, according to a transcripts of the court proceedings.
Every time the judge asked anything, he nodded affirmatively.
To begin with the judge read out to him his constitutional rights.
"You have the right under the Constitution of the United States to remain silent. Any statement made by you may be used against you in court, and you have the right not to have your own words used against you," the judge said.
Responding to a question, Dzhokhar said he cannot afford an attorney.
"No" he said when the judge asked "Can you afford a lawyer?" Thereafter judge Bowler provisionally appointed federal defender William Fick as his attorney.
"At this time, at the conclusion of the initial appearance, I find that the defendant is alert, mentally competent, and lucid. He is aware of the nature of the proceedings," the judge said towards the end of the court proceedings inside the hospital room.
In consultation with the federal prosecutors and the government appointed attorney for Dzhokhar, the judge determined May 30 as the date for court hearing.
Three people died and more than 200 were injured when two bombs exploded in quick succession at the Boston Marathon, last week.
The police has identified Dzhokhar and his 26-year-old elder brother Tamerlan, as the suspects.
Tamerlan, said to be the mastermind, died in a police gunfight on Thursday.
Indian-American attorney to prosecute Boston bomber
Boston bomber Dzhokhar not an enemy combatant: US
What public transport tickets COST across the world
US investigators start quizzing injured Boston suspect
Should pharma MNCs be peeved?