It could encourage some European compnies to resume trading with Iran after they stopped earlier this year for fear of being closed out of the US market.
The Iran nuclear deal was agreed in 2015 under Mr Trump’s predecessor Barack Obama, alongside Britain, China, France, Germany and Russia.
Under its terms Iran agreed to open its nuclear programme up to international scrutiny in exchange for reduced international sanctions.
But Mr Trump, a long-time critic, officially re-imposed the sanctions in August, three months after he announced was pulling the US out of the agreement.
A second round of measures was due to be announced next month.
Peter Hoekstra, the US ambassador to the Netherlands, where the court is based, said: “This is a meritless case over which the court has no jurisdiction. Even so, it is worth nothing that the Court declined today to grant the sweeping measures requested by Iran.
Iran said the court’s decision was a “victory for rule of law.”