The Sinn Féin leader has described Brexit as the "opportunity of a lifetime" to unite the island and transform the country.
Speaking at the Institute of International and European Affairs in Dublin, Mary Lou McDonald said the European Union could assist with Irish unity project by giving Northern Ireland MEPs observer status.
In her speech entitled 'Ireland and the EU after Brexit', she claimed all traditions in the North see Irish unity as the best way to re-enter the EU.
Ms McDonald also said it was not a question of 'if' but 'when' a referendum on Irish unity will be held.
She said there "cannot and will not be a hard border on the island of Ireland" and that Brexit has exposed the undemocratic nature of partition.
The Sinn Fein leader also said another no-deal scenario at the end of this year needs to be avoided.
She told the assembled audience that the European project is far from perfect, "for many ordinary working people the EU does not work for them but against them".
Ms McDonald said privatisation, federalism and the push for a militarized EU have left European citizens alienated from the EU and created distrust.
But she said she believed the EU could be a powerful force for good in the world if it changed direction and put citizens first. She said she believed Ireland could be at the fore in shaping this new direction.
Ms McDonald said the people and politicians of Northern Ireland have not consented to leaving the EU and are angry about this.
She said the Good Friday Agreement assumed continued membership of the EU and she said there is no good version of Brexit for Ireland North or South.
The Sinn Féin leader has said that Brexit has reshaped and recast Irish politics, highlighted the damage of partition and made it necessary to talk about reunification.
Speaking on the border hours before Britain leaves the EU, Mary Lou McDonald said the most effective way to protect Irish interests in the next phase of Brexit is to have Sinn Féin ministers in government both north and south.
She said that is a lot of anger and fear in border communities because the future is still very unclear.
Ms McDonald said its important Brexit does not become a partisan issue and said it is too serious an issue for any party to use to "score cheap political points".
She said Sinn Féin had worked constructively with the outgoing government to restore the Northern Assembly because they collectively understood they needed it protect the island from the threat of Brexit.
She said, regardless of the makeup of the next government, political parties need to work collectively. She said whoever is in government has a "mighty task ahead of them".
Asked if she had a preference for working with Leo Varadkar or Micheál Martin in this regard, she said she would work with anyone to protect the peace process.
"By God, we’ve worked with Boris Johnson so you know, we worked with Tories to make that happen".
She said today was a sad day and not an end point but very much the beginning. Ms McDonald said it is a day when the consent of the people of the North was set aside, something she described a "deeply worrying".
However she said there was no appetite or basis for a return to violence; "we have the democratic mechanisms to mediate this".
She said Sinn Féin needed to work with unionism and that the British government needed to deliver on their agreements.