"Following an in-depth investigation opened in July 2015, the (European) Commission has concluded that the acquisition will not give rise to competition concerns," the EU's powerful executive arm said in a statement.
The companies are "not particularly close competitors ... (and) the merged entity will continue to face sufficient competition from its rivals in all markets concerned," it said.
Brussels opened the investigation citing concerns the deal could lead to higher prices for consumers who are increasingly buying online and getting packages delivered directly to them.
The deal announced in April came two years after the Commission torpedoed a bid by FedEx's US rival UPS to buy TNT Express.
TNT Express went through extensive restructuring after the UPS bid failed, cutting 4,000 jobs.
FedEx employs more than 320,000 people worldwide with annual turnover of USD 47 billion.