The Court of Justice (ECJ) overturned a General Court ruling, which had said there was not enough evidence to keep travel bans and asset freezes on Hamas.
The lower court had said in 2014 the listing was based on media reports, not decisions by "competent authorities".
But the ECJ said such decisions were not needed to keep groups on the list.
In Wednesday's ruling, the Luxembourg-based ECJ said decisions by the competent authorities were only required for the initial listing of groups or individuals.
It said its verdict reaffirmed that the EU "may maintain a person or an entity on the list if it concludes that there is an ongoing risk of that person or entity being involved in the terrorist activities which justified their initial listing".
The ECJ added it was referring the case back to the General Court to examine the facts and arguments it did not consider in 2014.
In a separate ruling, the ECJ backed the General Court's ruling that the Sri Lanka's Tamil Tigers organisation should be removed from the blacklist.
The top court said that the military defeat of the separatist group in 2009 "represents a significant change in circumstances, one that is capable of calling in question the ongoing nature of the risk of the LTTE's (the Liberation Tigers of Tamil Eelam) involvement in terrorist activities".
The EU's terrorist list was drawn up after the 11 September 2001 attacks on the US, to enable the bloc to freeze a group's financial assets and improve the way police and justice officials co-operated.
The list was last updated in January, and now includes 13 individuals and 22 organisations.
Hamas has always argued it is a resistance movement rather than a terrorist organisation, although under its charter it is committed to Israel's destruction.
It is seen as a terrorist group by the EU, US, Canada and Japan.
After winning parliamentary elections in 2006, Hamas ousted its Fatah rivals from Gaza the following year and has since fought several conflicts with Israel.
The European Union's top court has ruled that the Palestinian Islamist group Hamas should remain on the 28-member bloc's terrorism blacklist.