The unit will provide a virtual and physical platform for European Union (EU) institutions and agencies to collaborate with member states and share resources through secure channels, Xinhua reported.
It will serve as part of the EU Cybersecurity Incident and Crisis Response Plan, the Commission said in a statement.
"The Joint Cyber Unit is a building block to protect ourselves from growing and increasingly complex cyber threats," Thierry Breton, Commissioner for the Internal Market, said.
Margrethe Vestager, the Commission's executive vice-president for a Europe fit for the digital age, added that "responding to threats in a coordinated manner is paramount."
The Commission said the unit will act as a platform to ensure an EU coordinated response to large-scale cyber incidents and crises, as well as to offer assistance in recovering from these attacks.
The unit will be established on a phased basis over four steps, with plans to be operational by June 2022 and fully established by June 2023, according to the statement.
The EU Agency for Cybersecurity will lead the efforts, which will be funded through the Digital Europe Programme.