"During the Brexit negotiations, the EU and Ireland must work together to minimise the impact," Juncker said after talks with Irish Premier Enda Kenny in Brussels.
"We don't want hard borders between Northern Ireland and the Republic" of Ireland, he said.
Ireland is set to be the only EU country to share a land border with Britain after Brexit, fuelling concerns in Dublin about the implications for trade and security.
During the troubles in Northern Ireland, the border was festooned with military outposts and controls which were later removed as part of the 1998 Good Friday peace accords.
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"There should not be a return to a hard border and there won't be," he said.
Kenny also said Ireland wanted the language of the Good Friday Agreement, which has international status since it is lodged at the United Nations, to be included in a Brexit settlement.
"We do not want to see the Good Friday Agreement damaged in any way," he said, citing provisions on Northern Ireland's right to decide its own future, including reunification.
For his part, Juncker said the peace deal was "an important agreement ... The Irish and British have worked hard to have it and in no way should it become under risk."
British Prime Minister Theresa May is expected to trigger Article 50 negotiations by the end of next month, triggering two years of what promise to be difficult and complex negotiations.
Kenny and May have said previously they, too, do not want a return to the fixed border between the two major trading partners.