In a statement issued following weeks of unrest and tensions over Brexit, the monarch said it was clear that "equality and understanding" cannot be taken for granted.
She added: "This anniversary reminds us of our complex history, and provides an opportunity to reflect on our togetherness and our diversity.
"In Northern Ireland today, there is, perhaps, more than ever, a rich mix of identities, backgrounds and aspirations, and an outward-looking and optimistic mindset.
"The political progress in Northern Ireland and the peace process is rightly credited to a generation of leaders who had the vision and courage to put reconciliation before division. But above all, the continued peace is a credit to its people, upon whose shoulders the future rests."
Boris Johnson described the centenary as a "very significant" milestone in Northern Ireland's history.
He added: "Throughout 2021, in its centenary year, the government will continue to showcase all the brilliant things Northern Ireland contributes to the rest of the UK and the world, from its world-class Fintech industry and research capabilities, to its inspiring young people, and its vibrant culture of arts and sport.
"It is also important that we pause to reflect on the complex history of the last 100 years. People from all parts of Northern Ireland, the Republic of Ireland, the United Kingdom and across the globe, will approach this anniversary in different ways, with differing perspectives.
"While this is a moment of shared reflection, it is also an important opportunity to come together to celebrate Northern Ireland and build towards a better and even brighter future for all its people."
Northern Ireland was created on 3 May 1921 when the Government of Ireland Act came into effect, partitioning the island of Ireland into two separate areas.
Though there will not be any major celebrations on Monday due to the Covid-19 pandemic, there are plans to mark the centenary later in the year, including with tree-planting projects.
Every school will be presented with a native tree to plant in their grounds, while an extensive young people’s programme will explore what the future will look like in the next 100 years.
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