She said foreign ministers from the 28 European Union member states decided to appeal the decision at a meeting in Brussels today which is more widely focused on the Islamist threat after last week's Paris attacks.
"This ruling was clearly based on procedural grounds and did not imply any assessment by the court of the merits of designating the Hamas as a terrorist organisation," Mogherini said in a statement.
The ministers have "now decided to challenge some of the findings of the court regarding the procedural grounds to list terrorist organizations," she said.
Hamas, which has been in power in the Palestinian territory of Gaza since 2007, had appealed against its inclusion on the blacklist on several grounds.
In Gaza City, Hamas spokesman Sami Abu Zuhri told AFP that the decision to appeal "is an immoral step, and reflects the EU's total bias in favour of the Israeli occupation."
Hamas's military wing was added to the European Union's first-ever terrorism blacklist drawn up in December 2001 in the wake of the September 11 attacks on the United States.
The EU court based in Luxembourg said last month that the freeze on Hamas's funds will also temporarily remain in place for three months pending any appeal by the EU.
The Hamas ruling had threatened recent Brussels attempts to play a bigger role in reviving the moribund Middle East peace process, with Israeli premier Benjamin Netanyahu saying it showed Europeans had learned nothing from the Holocaust.
A vote by the European Parliament backing the recognition in principle of a Palestinian state just hours after the Hamas decision, following a series of such votes in European nations, added fuel to the fire.