Voting began at 07:00 BST and ended at 22:00.
Foyle was the first local constituency to declare a result, with 78.3% voting to Remain in the European Union out of a 57% turnout.
The outcome of the Northern Ireland poll will be announced at the Titanic centre in Belfast.
The ballot paper asked voters: "Should the United Kingdom remain a member of the European Union or leave the European Union?"
Electoral staff in Northern Ireland are spread across eight different count centres and have the task of counting the votes in more than 1,300 ballot boxes.
There were 619 polling stations across Northern Ireland and more than 1.25m people were registered to vote.
Declarations for parliamentary constituencies will be made throughout the night, with the final Northern Ireland and UK-wide result due by breakfast time on Friday.
The official declaration will be made at Manchester Town Hall.
There will be comprehensive coverage online, with live updates throughout polling day and overnight, as well as up-to-the minute results.
And from 06:00 BST on Friday, BBC News NI will have a live page dedicated to the outcome and reaction.
BBC One, the BBC News Channel and BBC Parliament are broadcasting a results show hosted by David Dimbleby alongside BBC experts and special guests.
Coverage continues throughout the night and Sophie Raworth, Andrew Neil and Victoria Derbyshire pick up the coverage on Friday morning.
The polls have closed in the EU referendum in Northern Ireland with counting under way.