The refiling in U.S. District Court in Austin, Texas, came a day after Judge Sam Sparks dismissed the cyclist's first restraining order request, chastising its length -- 80 pages -- and calling much of it "totally irrelevant" to the charges against Armstrong.
Armstrong's attorneys shortened Tuesday's filing by more than 80 pages, the Los Angeles Times reported.
In the motion, Armstrong asks Sparks to halt the USADA case against him on constitutional grounds, asserting his Fifth Amendment rights had been violated.
The cyclist claimed the investigation was "causing irreparable injury" to him and asks that the agency be kept from stripping him of his seven Tour de France championships.
It seeks reimbursement for legal fees and "further equitable relief."
The anti-doping agency, stating it had testimony from 10 anonymous cyclists and new -- but unrevealed -- analysis of blood tests taken in 2009-2010, filed formal charges against Armstrong June 28, alleging he participated in a doping conspiracy for at least 14 years.