The move has been welcomed by animal welfare activists, with Liberal MEP Catherine Bearder calling it "a vitally important step for the conservation of lions and other endangered species".
A survey revealed last year that, tragically, there are only about 400 lions left in the wild in west Africa.
Up until now, the convention on international trade in endangered species of wild fauna and flora (Cites) listed lions as a protected species, whereby trade in lion parts was strictly regulated.
However, these regulations do not apply to hunting trophies, as they are considered "household and personal effects" by the treaty.
Bearder explained that "this derogation had allowed people to use the EU as a route for trading animal parts for use in quack medicines".
She added that "this glaring loophole had allowed the import of hunting trophies from lions which are on the brink of extinction".
Now, the commission is set to ban imports of lion hunting trophies into the EU from several west African countries, such as Burkina Faso and Benin.
"This glaring loophole had allowed the import of hunting trophies from lions which are on the brink of extinction" - Catherine Bearder
The UK deputy was pleased that these rules would bring "better protection for lions and other endangered species", but warned that "we must remain vigilant and ensure they are enforced by clamping down on the criminal gangs that operate the illegal wildlife trade".
Between 2008 and 2012, nearly 1500 lion hunting trophies were imported into the EU. While the majority came from South Africa, where most hunted lions are bred in captivity, some were shot in the wild and came from highly endangered populations.
80 per cent of western African hunting trophies of endangered lion species were imported to France.
Catherine Bearder has now called on the EU to "ask all African countries to justify trophy hunting and prove it is being done sustainably".
LionAid trustee Pieter Kat said, "we hope that now the EU can request much more information from African source countries about the sustainability of trophy hunting of species like lions that is in rapid decline to justify the issuance of import permits".
LionAid is a UK based organisation that campaigned for the new regulations.