Juncker, a former prime minister of Luxembourg, also wished Macron "good luck" in the May 7 second round of voting, when he will face far-right challenger Marine Le Pen, according to the projections.
"@JunckerEU congratulated @EmmanuelMacron for his result in the first round and wished him good luck for the next," according to Juncker's tweet, which he sent in French.
Other EU officials also welcomed Macron's strong showing. Many officials in Brussels had privately expressed concerns about Le Pen, a eurosceptic who has taken a hard line on immigration.
"To see the flags of #France and the EU greet the result of @emmanuelmacron, it's the hope and future of our generation," tweeted EU foreign policy chief Federica Mogherini, a former Italian foreign minister.
Michel Barnier, the European Commission's chief negotiator on Britain's withdrawal from the EU, hinted at concerns that Le Pen could lead France away from the 28-nation bloc.
"Patriot and European, I will put my trust in Emmanuel Macron on May 7. France must remain European," the Frenchman tweeted.
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