Mogherini, who has pushed hard for the EU to take on an increased military role, said foreign and defence ministers of the 28 member states "unanimously" backed the project.
"Today we decided to establish a MPCC (Military Planning Conduct and Capability facility) which will command the EU's non-executive military missions," she told reporters.
The facility will initially run three operations -- civil-military training missions in Mali, the Central African Republic and Somalia -- which do not involve the use of force, other than in self-defence.
These executive operations have their own command centres which will remain separate.
Mogherini said the decision was a huge step forward for the EU after decades of division over what defence role the bloc should take on -- with exit-bound Britain having long opposed it.
She spoke of a "certain pride" about the agreement.
"This is one of the fields where traditionally we have had in the history of the European Union more divisiveness -- since the Fifies we were struggling in the defence field," she said.
But top EU officials, including Mogherini, have had to repeatedly issue reassurances that the bloc is not going to undercut NATO as the primary defence for Europe.
Besides Britain, many of the former Communist states of eastern Europe such as Poland and Hungary have argued consistently that NATO must come first, given the need for US support in facing a more assertive Russia.
European Commission head Jean-Claude Juncker called for a common EU defence headquarters in September after the Brexit vote, resurrecting an idea that had circulated in the EU for years.
The new facility will initially have a small staff of around 30 and come under the EU's existing military structures.
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