During a tense exchange with Mr Moussaoui, Judge Leonie Brinkema said she wanted to give him more time to consider his decision to enter the guilty plea, despite Mr Moussaoui's protestations.
"You have changed your mind so many times in the past," she said.
Mr Moussaoui, a 34-year-old French citizen, was arrested in August last year and indicted in December on six counts of conspiring to commit acts of international terrorism.
Admission
Ms Brinkema originally entered a not guilty plea on Mr Moussaoui's behalf.
However, Mr Moussaoui, who is representing himself, said he wanted to plead guilty, insisting he knew what he was doing.
He admitted he was a member of the al-Qaeda organisation, pledged his allegiance to wanted Osama Bin Laden and claimed he had "certain knowledge" of the 11 September attacks.
"You are admitting what the government is claiming you did," said Judge Brinkema.
She scheduled a new hearing for 25 July and asked Mr Moussaoui to think about his decision for a week.
"I don't need (a week)," Mr Moussaoui replied. "I've been thinking about it for months".
Correspondents say Ms Brinkema's caution regarding Mr Moussaoui's case is an attempt to ensure he is aware of the workings of the US justice system.
In criminal trials, defendants often negotiate their guilty pleas in exchange for lesser charges or more lenient sentences.
Death penalty
The court hearing in Virginia was scheduled after the US Government obtained a fresh indictment against Mr Moussaoui.
The original indictment was amended to include "aggravating circumstances" that would enable the US Government to seek the death penalty for Mr Moussaoui.
US prosecutors amended the indictment after the Supreme Court ruled last month that juries, not judges, must make the crucial decisions on life or death.
Mr Moussaoui has been referred to by some US officials and media as a possible "20th hijacker" who was meant to have been on board one of the planes that smashed into the World Trade Center and Pentagon on 11 September.