The case was brought by the same atheist whose previous battle against the words "under God" was rejected last year by the Supreme Court on procedural grounds.
U.S. District Judge Lawrence Karlton ruled that the pledge's reference to one nation "under God" violates school children's right to be "free from a coercive requirement to affirm God."
Karlton said he was bound by precedent of the 9th U.S. Circuit Court of Appeals, which in 2002 ruled in favor of Sacramento atheist Michael Newdow that the pledge is unconstitutional when recited in public schools.
CBS News Correspondent Wyatt Andrews reports that last year, the Supreme Court ducked a direct ruling because it said Newdow lacked custody of his daughter, he lacked the standing to sue. Newdow, an attorney, simply found two parents who do have custody and now he's back in business.
Newdow, an attorney and a medical doctor, filed an identical case on behalf of three unnamed parents and their children. Karlton said those families have the right to sue.
"Imagine every morning if the teachers had the children stand up, place their hands over their hearts, and say, 'We are one nation that denies God exists,"' Newdow said in an interview with AP Radio after the ruling.
"I think that everybody would not be sitting here saying, 'Oh, what harm is that.' They'd be furious. And that's exactly what goes on against atheists. And it shouldn't."
Karlton, ruling in Sacramento, said he would sign a restraining order preventing the recitation of the pledge at the Elk Grove Unified, Rio Linda and Elverta Joint Elementary school districts in Sacramento County, where the plaintiffs' children attend.
The order would not extend beyond those districts unless it is affirmed by the 9th Circuit, in which case it could apply to nine western states, or the Supreme Court, which would apply to all states.
The decision sets up another showdown over the pledge in schools, at a time when the makeup of the Supreme Court is in flux.