The General Court of the European Union said in a statement on Wednesday that the original conclusion of the movement was based not on reliable sources, but conclusions from the media and internet reports.
"The General Court finds that the contested measures are based not on acts examined and confirmed in decisions of competent authorities, but on factual imputations derived from the press and the Internet," it said.
The second-highest court in the bloc added that such a decision had to be made based on previously established facts by competent authorities.
The court, however, said that its ruling does "not imply any substantive assessment of the question of the classification of Hamas as a terrorist group."
The freeze on Hamas's funds will also temporarily remain in place for three months pending any appeal by the EU, the Luxembourg-based court said.
The move comes as the European Parliament is expected to recognize Palestine as an independent state on Wednesday.
The court ruling comes upon an appeal filed by Hamas against its inclusion in the European Union's list of terrorist organizations.
The EU blacklisted the political wing of Hamas in 2003.
Hamas's military wing, the Ezzedine al-Qassam Brigades, had been added to the EU’s terrorism blacklist in December 2001.
On Tuesday, a senior Israeli politician slammed the EU for planning to remove Hamas from its blacklist of terrorist groups.
"The Europeans must believe that their blood is holier and Israeli blood is cheap, otherwise you cannot understand how the court will discuss the removal of Hamas from the list of terrorist organizations,” said Danny Danon, a Likud party member of the Israeli parliament (Knesset).
He also described the scheduled vote as “hypocrisy.
The Palestinian resistance movement controls the Gaza Strip, that has been under crippling Israeli siege since 2007.