James Brokenshire is travelling to Brussels for meetings with senior EU Commission officials and permanent representatives of EU member states.
He said he wanted Northern Ireland's "particular circumstances" recognised.
He restated the UK government's aim of achieving as "frictionless" a border as possible with the Republic of Ireland.
"I am acutely aware that the ability to move and trade freely across the border is an essential part of daily life for people and businesses on both sides of the border," he said.
Mr Brokenshire also repeated his intention to protect the Common Travel Area between Great Britain and the island of Ireland.
He said: "We want to get the best possible deal for the UK and the best possible deal for Northern Ireland within the UK, recognising Northern Ireland's particular circumstances"
"That is the prime reason for my visit - to ensure Northern Ireland's interests are protected and advanced."
After Brexit, Northern Ireland will be the only part of the UK that will share a land border with an EU member state.
How that land border will be monitored or policed is causing concern, particularly among businesses and border communities.
A convoy of protesters staged a demonstration at the border between County Louth and County Armagh earlier this month.
It was also revealed that the Irish government has begun to identify border locations where customs checkpoints could be set up, as part of its Brexit contingency plans.
However, Taoiseach (Irish Prime Minister) Enda Kenny has stated said he is confident the EU would not allow "one of the most divisive borders in the world" to be re-imposed.
The secretary of state has said he will "ensure Northern Ireland's interests are protected" when he meets leading EU figures for Brexit talks on Wednesday.