"The reference that the (trade agreement) enter into force on 1 January 2016 was not contested by the Russian delegation," Trade Commissioner Cecilia Malmstroem said after talks with Russian and Ukrainian officials.
Malmstroem added that there was a "clear understanding" that the deal would not be amended and would now be implemented on time.
Russia had claimed that the so-called EU-Ukraine Deep and Comprehensive Free Trade Agreement will damage its own important economic ties and interests in its Soviet-era satellite.
The deal was finally agreed in 2014 and was originally due to come into effect in January this year.
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But in September the EU postponed implementation for a year to support peace efforts as a first ceasefire accord was negotiated in the Ukraine conflict between government forces and pro-Russian rebels.
In return, Russia promised to hold off on the retaliation it had threatened if the EU and Ukraine had gone ahead with the trade pact without resolving its concerns.
The EU still has tough sanctions in place against Russia over the Ukraine conflict.