Last month, US District Judge Sam Sparks, in Austin, Texas, dismissed Armstrong's original bid to stop the US Anti-Doping Agency (USADA) from proceeding with its case, calling the lawsuit a "lengthy and bitter polemic." But Sparks allowed Armstrong's lawyers to file an amended lawsuit.
On Monday, Sparks threw out the revised complaint, though he dismissed it "without prejudice," meaning Armstrong can try again. A lawyer for Armstrong could not immediately be reached for comment.
Accusations of doping have dogged Armstrong, who won seven straight Tour de France championships between 1999 and 2005 when he ascended to the top of the cycling world after overcoming cancer.
In a statement, USADA chief executive Travis Tygart said the agency was pleased with the ruling and defended its process for investigating doping charges, saying it had "protected the rights of athletes for over a decade."
The USADA, a quasi-governmental agency created by the US Congress in 2000, formally charged Armstrong in June with doping and taking part in a conspiracy with members of his championship teams. Five other cyclists have been accused of conspiring with Armstrong over the course of 14 years to hide doping activity.
The agency said in a letter to Armstrong that it has blood samples from 2009 and 2010 that are "fully consistent" with doping.
In the letter, which was published in the Washington Post, the agency said it also has at least 10 former team-mates and colleagues of Armstrong who will testify he used doping drugs during races from 1999 to 2005.
Lawyers for Armstrong contend the USADA gathered evidence by threatening to ruin the careers of fellow cyclists who have agreed to testify against him. Lawyers for Armstrong also argue that the agency's rules violate Armstrong's right to a fair trial and that it lacks proper jurisdiction to charge him.
In February, the Justice Department dropped an investigation centred on whether Armstrong and his team-mates cheated the sponsor of their bike racing team, the US Postal Service, with a secret doping program.
Armstrong's attorneys contend that he has "passed every drug test ever administered to him in his career - a total of 500 to 600 tests... more drug tests than any athlete in history."
They say the International Cycling Union has proper jurisdiction in the case.
The USADA charges will be considered by its own arbitration process. Any penalties would be binding within the sport, but federal courts have the power to overrule the agency.