The EU made a clear play to pass talks off as positive – but huge issues were left unanswered.
European Council President Donald Tusk said: "Fundamental western values of freedom, human rights unite US and EU."
However, Mr Tusk said later both sides had expressed "different" opinions on climate change, Vladimir Putin's Russia, and global trade.
The pair appeared to look tense in pictures taken on Thursday morning, including one in which they are locked in a stare across the meeting table.
Tusk said in a televised statement the two leaders agreed on countering militant violence and on relations with Ukraine.
Donald Trump looks tense heading in to meeting with Donald Tusk
Awkward! Donald Tusk and Donald Trump stare at each other across a table
The rocky start could be a sign of trouble ahead for the rest of the week's meetings.
At a summit of leaders of the Group of Seven (G7) world powers in Sicily on Friday and Saturday, Trump will be pressed to reaffirm the US commitment to free trade and to keep the United States in the Paris agreement on climate change.
The White House has said a decision on the climate deal will come after the visit.
Donald Trump and Donald Tusk – The pair looked tense across the table in Brussels
Get Quotes on Home Insurance
Some issues remain open like climate and trade
Mr Tusk said in Brussels after he and EU chief executive Jean-Claude Juncker met Trump for an hour: "We discussed foreign policy, security, climate and trade relations.
"My feeling is that we agreed on many areas, first and foremost on counter-terrorism."
"But some issues remain open like climate and trade and I am not 100 percent sure that we can say today – 'we' means Mr President and myself – that we have a common position, common opinion, about Russia, although when it comes to the conflict in Ukraine it seems that we were on the same lines."
Donald Trump in Brussels
Thu, May 25, 2017
Donald Trump has arrived in Brussels for talks with European leaders at the European Council
1 of 10
Donald Trump talks with President of the European Council, Donald Tusk
However, Jean Claude JUnker tried to gloss over the clear divisions by insisting talks were successful.
The European Commission tweeted: "Good, cordial and friendly discussion with @POTUS. Overall, constructive.
"Agreed to work on joint action plan on trade."
US business leaders have generally supported the way that the EU's single market rules offer efficiencies for exporters and services firms selling into the continent.
However, there are many hurdles to cross before an agreement can be made final.
Both Donald Tusk and Donald Trump looked tense as they met in Brussels
President Trump has previously been highly critical of the European Union – and praised Britain for Brexit.
However, he later called it "wonderful".
Trump, also once called labelled Brussels a "hellhole".
The president and wife Melania arrived in Brussels on Wednesday evening before meeting with the Royals.
Streets were closed off for the arrival of Mr Trump and the First Lady who headed first to the Belgian royal palace to meet King Philippe and Queen Mathilde.
Trump then met Prime Minister Charles Michel.
Donald Trump arrives in Brussels after calling it a