Vladimir Putin will meet the new head of the European Commission, Jose Manuel Barroso, in talks originally scheduled for the beginning of the month.
Russia and the EU have differed sharply over Ukraine's troubled election.
Kremlin official Sergei Yastrzhembsky said he hoped the two sides would reach some understanding on the issue.
Thursday's summit was due to have taken place early in November but a wrangle over the new Commission's line-up at the European Parliament caused it to be postponed.
The scheduled agenda focuses broadly on bilateral relations including cross-border policing and the liberalisation of visa arrangements.
Other items include access to Russia's Kaliningrad exclave - surrounded entirely by EU states since enlargement - and the situation in the war-torn Russian region of Chechnya.
The summit is being held in the Netherlands, which currently holds the EU's rotating presidency.
'Consequences'
Mr Yastrzhembsky, who advises President Putin on EU matters, told a Moscow radio station that he accepted that the EU might raise Ukraine at the talks.
The Russian president moved swiftly to congratulate Ukrainian government candidate Viktor Yanukovych on his victory in the presidential election before official results were released.
The EU has voiced dismay over a result widely believed to have been falsified and rejected by opposition candidate Viktor Yushchenko, whose supporters have been holding mass rallies in protest.
Mr Barroso urged a "serious, objective" review of the election result and warned of "consequences" for ties with Ukraine otherwise.
On scheduled summit business, Sergei Yastrzhembsky said Russia was not yet ready to move to a visa-free regime with the EU but was looking to sign an agreement on easing visa regulations.
Russia and the EU were "going round in circles" over Chechnya, he added, and on Kaliningrad, he said the Baltic territory was becoming less of a problem between Russia and the EU.