The award marks a remarkable rise for the 24-year-old who only made his international debut in 2009 against Fiji but is now an established part of Declan Kidney's set-up, starting every one of Ireland's 2011 RBS 6 Nations matches.
O'Brien beat his Leinster teammates Jamie Heaslip and Isa Nacewa to the award while Italian captain Sergio Parisse and Northampton's Soane Tonga'uiha were also shortlisted.
And O'Brien's trophy cabinet could yet have another new arrival with Leinster facing off against rival Munster in the Magners League Grand Final this weekend.
"It's been a fantastic year for me, and more importantly for Leinster," said O'Brien. "It's great to be presented with an award like this, but it has more to do with the team than it has to do with me.
"Hopefully, this is only the start rather than the end of our success in Europe, and of course, we've got another trophy to aim at this weekend."
ERC chief executive Derek McGrath says O'Brien was the obvious choice for his three man-of-the-match awards in the Heineken Cup this season.
He said: "Sean was an inspirational character at the heart of the Leinster pack in their victorious Heineken Cup season and proved himself to be a major force both as a ball carrier and defender.
"He played across the back row, scored vital tries and picked up three Heineken Man of the Match awards. His power, athleticism and consistency over the course of the Heineken Cup made him an excellent choice for the ERC European Player of the Year Award."