BRUSSELS—The European Union’s second-highest court ruled Monday that the bloc had unfairly targeted a former top aide to ex-Ukrainian President Viktor Yanukovych with an asset freeze in early 2014, saying there was little evidence at the time that Andriy Portnov was guilty of the allegations.

Mr. Portnov, a close adviser to Mr. Yanukovych, had already beendropped from the EU’s sanctions list in March of this year but had proceeded with the challenge in the EU’s General Court. He was one of 23 Ukrainians originally targeted with an EU asset freeze in March 2014 for alleged misappropriation of funds in the chaotic days after Mr. Yanukovych fled to Russia amid huge street protests.

There have long been concerns among EU officials about the legal strength of some of the sanction listings. In March, after diplomats complained that Kiev hadn’t provided enough evidence against some of the targets, the EU dropped several people from the list.

Monday’s ruling could have repercussions for some of the 17 people still targeted by the asset freeze, many of whom have lodged their own challenges in EU courts. The former president, still in Russia, and his surviving son are among those people.

The ruling could also make it harder for the EU to act swiftly in the future when governments collapse to prevent stolen funds from being taken abroad, diplomats said.

The European Council, the body which represents member states, said Monday it was studying the judgment and had no further comment at this stage. It could still appeal the decision. Ukraine’s presidential office and foreign ministry didn’t respond to a request for comment.

In Monday’s ruling, the court said the EU appeared to have acted in 2014 to freeze Mr. Portnov’s assets solely on the basis of a letter from Kiev’s Public Prosecutor stating its preliminary investigation had allowed it “to establish misappropriation of sizable amounts of State funds and the subsequent illegal transfer of these funds outside Ukraine.”

The court said the letter provided no details concerning the facts alleged against Mr. Portnov. Subsequent documentation was provided to the court. Nonetheless, the bloc itself decided in March there was too little evidence against him.

With the EU pressing Kiev to provide more evidence, Ukrainian prosecutors have in recent months launched criminal proceedings against most of the 17 people now left on the EU’s Ukraine corruption list. Two former ministers, Olena Lukash and Dmytro Tabachnyk, are still listed by the EU as being under investigation. Ms. Lukash’s husband was a former head of foreign intelligence in Ukraine.

In recent years, the EU has faced a range of legal defeats on its sanction decisions after cases lodged by Syrian and Iranian companies and people.

There are also pending challenges to EU sanctions decisions by Russian people and companies targeted because of the conflict in eastern Ukraine.

The court has frequently accused EU governments of failing to provide enough evidence to back up its decisions, although in a bid to address this, the European Court of Justice moved earlier this year to make it easier for capitals to share confidential evidence with its judges.

Diplomats said Monday’s ruling could make it harder for the EU in the future to move swiftly to prevent transfer of assets abroad when other regimes collapse. In addition to Ukraine’s crisis, the bloc moved rapidly in 2011 to prevent stolen funds from being moved out of Egypt when the Mubarak regime fell and out of Tunisia when the regime of Zine El Abidine Ben Ali collapsed.

Taking weeks to compile sufficient evidence to back up possible evidence of corruption could make it next to impossible to act effectively in the future. In the past, some of the court’s legal advisers have recognized that initially, a lower standard of evidence, can be provided in such cases even if subsequent decisions to roll over penalties need firmer backing.

EU Court Raises Fresh Doubts Over Bloc’s Sanctions