BRUSSELS—European Union and Japan’s leaders vowed to fast-track negotiations in an effort to sign a trade pact as soon as this year, seeking to counter U.S. protectionism while boosting exports to bolster tepid growth in their economies.

Japanese Prime Minister Shinzo Abe met with European Council President Donald Tusk and European Commission President Jean-Claude Juncker in Brussels on Tuesday, pledging to deepen economic, political and security ties in an effort to jointly address global challenges.

The leaders described their prospective free-trade agreement as a flag-bearer for global commerce when protectionism was growing. They didn’t mention President Donald Trump by name but his criticism of multilateral agreements has unsettled U.S. trading partners.

“We believe this agreement is necessary…because we believe in free, fair and rules-based trade,” Mr. Juncker said. “We will continue to look out toward the world, rather than return to isolationism.”

Mr. Abe’s visit to the EU capital follows last week’s Group of 20 meeting, where the U.S. pressured the world’s largest economies to scrap a stance against protectionism. The Japanese premier’s trip also takes place a week before Britain triggers talks to exit from the EU, undermining a 60-year push toward trade-led integration spanning 28 countries.