"In respect of all issues, the court dismissed the applications," judge Paul Maguire said.
With other legal challenges under way elsewhere in the United Kingdom, the verdict will be closely monitored by politicians and financial markets.
A cross-party group of politicians claimed Northern Ireland should have a veto on leaving the European Union, and the Northern Irish Assembly should have a say on whether to trigger exit negotiations with Brussels.
The claim was brought alongside a linked challenge on the impact of Brexit on the Northern Irish peace process.
The verdict comes after three days of hearings earlier this month.
"While the wind of change may be about to blow, the precise direction in which it will blow cannot yet be determined so there is a level of uncertainty, as evidenced by the discussion about how the Northern Ireland land border with Ireland was affected by withdrawal from the EU," said Maguire.
In the June 23 referendum on EU membership, 52 percent voted for the UK to leave the European Union. Within Northern Ireland, 56 percent voted to stay.
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