The Prime Minister said she was working to get a full deal negotiated before Brexit day, but acknowledged it can not be signed until after the UK's withdrawal, expected on March 29 2019.
But the precise terms of the transition phase are the subject of the next set of negotiations.
Mrs May's comments came as the commission put forward proposals for a transition period which would last from Brexit day on March 29 2019 to the end of December 2020.
British Prime Minister Theresa May, who headed off a new parliamentary rebellion over Brexit as Barnier spoke, faces a fresh row over the proposed European Union timeline as she has called for a transition period that is three months longer.
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Talks on the post-Brexit transition period are to start in January, while negotiations on the future relationship between Britain and the European Union, including steps towards an eventual trade deal, are due to begin in March.
Barnier appeared to throw the Brexiteers a bone on one of their key issues, however, saying that while Britain would be excluded from talks on fishing quotas during the transition, there would be "specific procedural arrangements" to give it a voice.
Talks on a transition period are due to start in January after a green light from European Union ministers, with Britain hoping for an agreement on the main principles by March.
Given the potential pitfalls, "although May will be reluctant to extend Article 50 negotiations or the length of the transition. there is a significant probability she will have to", said analyst Rahman.
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THE final Brexit deal must allow Britain to strike "ambitious" trade deals around the world while having the "best possible" access to the EU, Theresa May has said.
The Bank of England, seeking to protect the City of London's status as a global financial hub, said it would spare European banks costly capital rules after Brexit but warned of "consequences" if negotiations with Brussels turned sour.
This could lead to a political declaration in October 2018 outlining the shape of the future relationship, but falling some way short of the full free trade agreement of the type being sought by Mrs May.
Guidelines covering the future relationship will be presented to the leaders of the remaining 27 states at a European Council summit in March, Mr Barnier said.
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Separate negotiations on the post-Brexit relationship between the EU and United Kingdom will be presented for adoption by the leaders of the remaining 27 EU states at a scheduled European Council summit in March, said Mr Barnier.