The party, which has only three known members, is very unlikely ever to win a seat in parliament - it would need around 60,000 votes, and pollsters estimate it would get fewer than a thousand.
But opponents had asked The Hague District Court to bar the party from registering for national elections in November, arguing that children have the right not to be confronted with the party's platform.
He noted that the PNVD party, the Dutch abbreviation of Brotherly Love, Freedom and Diversity, had not committed a crime, but was calling for a change in the law.
The party sparked outrage when it proclaimed its existence in late May, but prosecutors declined to prosecute its members as a threat to public order.
None of the party's members was in court for Monday's brief ruling.
Anke de Wijn, an attorney representing the party's opponents, said the pedophiles were abusing Dutch tolerance.
As of Monday, the PNVD's known members were a president, a secretary and a treasurer, as required under Dutch law. In order to stand in elections scheduled for Nov. 22, it will have to submit a list of candidates and the signatures of at least 30 supporters to get on the ballot in any one of the country's 19 voting districts.
Ireen van Engelen of the Solace Foundation, which researches pedophilia, said the party likely would fail to register for the elections because pedophiles seek anonymity.
Protesters picketed outside the courtroom when the case was heard on July 7, but stayed away from Monday's ruling.
The treasurer of the PNVD, Ad van den Berg, 62, was convicted of molesting an 11-year-old boy in 1987. He was fined and given a suspended prison sentence. After his background became known last month, he was chased from the trailer park where he lived in the city of Oostvoorne.
The party's Secretary Norbert de Jonge, 28, was evicted from the University of Nijmegen, where he was studying child education, when his involvement became known.
The legal age of consent in the Netherlands is 16.
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