The commission took the action to help protect bees.
But BASF officials contend that the bee decline is caused by multiple factors and that fipronil use is not one of those, according to a news release.
The Limburgerhof, Germany-based chemical manufacturer has said the EU Commission did not consider all of the scientific evidence available when making its decision.
As a result, it violated EU pesticide legislation.
The legal challenge was filed with the General Court of the EU.
Fipronil belongs to the Insecticide Resistance Action Committee's group 2.
Neonicotinoids, which also have been targeted as a contributor to honeybee decline, belong to the IRAC group 4A.
Fiprionil is found in many insecticides, including those used for field crops, cockroaches, fleas and ticks on pets (Frontline) and termites (Termidor).